Psyllid ID: psy15160

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340-------350-------360------
Protein Sequence
MAGFTQSALISKLEELNASQQSIQTLSLWLIHHRKHHSTIVKTWIDEVEKADDHRKLTLMYLANDVIQNSKKKGPEYGKEFGHVLKQAFVSVGDVHCSEKTRSSLSRILNIWEERGVYDKQQIASFRTAFNAALEPQTKRRKLSESNTEVLYDVDGNVPIGYFTFFHIDGKGRRNKYDKKQAFVSVGDVHCSEKTRSSLSRILNIWEERGVYDKQQIASFRTAFNAALEPQTKRRKLSESNTEVLYDVDELETSASSDANIREKIAKLPPEVSEIQLLSKVQGKNITGQPDRVAAENLSIQVNEAVDLLTNYNTRLVTEMEDRKRASAMLKDYIAAQRELLEQAEQRLEVSETEIFLFLKKFDGEY
Secondary Structure (PSIPRED)
cccccHHHHHHHHHHcHHHHHHHHHHHHHHHHcHHcHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHHHHccccHHHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHcccccHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHcccHHHHHHHHHHHHHHcccHHHHHHHccccHHHHHHHHHHHcccccccHHHHHHHHccccccHHHHHHHHHHcccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccc
Secondary Structure Prediction (SSPRO)
cccccHHHHHHHHHHHccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccHHHHHHHHHHHHHHHHccHHHHHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHHHcccccHHHHHHHHHHHcccccccccccccccccccHHHHHcccccHHHHcHHHHHHHHHHHHcccccHHHHHHHHHHHHccHcccHHHHHHHHHHcHHHHHHHHHHHHHHHHHcHHHHcccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccHHHccccccccccccccccccccHHHHcccccccHHHHHHHHcccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHEHccccc
Coil and Loop (DISEMBL)
MAGFTQSALISKLEELNASQQSIQTLSLWLIHHRKHHSTIVKTWIDEVEKADDHRKLTLMYLANDVIqnskkkgpeygkeFGHVLKQAFVSVgdvhcsekTRSSLSRILNIWeergvydkqQIASFRTAFNaalepqtkrrklsesntevlydvdgnvpigyFTFFhidgkgrrnkydkkqafvsvgdvhcsekTRSSLSRILNIWeergvydkqQIASFRTAFNaalepqtkrrklsesntevlydvdeletsassdANIREKIaklppevsEIQLLSKVqgknitgqpdrVAAENLSIQVNEAVDLLTNYNTRLVTEMEDRKRASAMLKDYIAAQRELLEQAEQRLEVSETEIFLFLKKFDGEY
Flexible Loop (DISEMBL)
MAGFTQSALISKLEELNASQQSIQTLSLWLIHHRKHHSTIVKTWIDEVEKADDHRKLTLMYLANDVIQNSKKKGPEYGKEFGHVLKQAFVSVGDVHCSEKTRSSLSRILNIWEERGVYDKQQIASFRTAfnaalepqtkrrklsesntevlydvdgnvpIGYFTFFHIDGKGRRNKYDKKQAFvsvgdvhcsektrsSLSRILNIWEERGVYDKQQIASFRTAfnaalepqtkrrklsesntevlydvdeletsassdaniREKIAKLPPEVSEIQLLSKVQGKNITGQPDRVAAENLSIQVNEAVDLLTNYNTRLVTEMEDRKRASAMLKDYIAAQRELLEQAEQRLEVSETEIFlflkkfdgey
Low Complexity Region (SEG)
MAGFTQSALISKLEELNASQQSIQTLSLWLIHHRKHHSTIVKTWIDEVEKADDHRKLTLMYLANDVIQNSKKKGPEYGKEFGHVLKQAFVSVGDVHCSEKTRSSLSRILNIWEERGVYDKQQIASFRTAFNAALEPQTKRRKLSESNTEVLYDVDGNVPIGYFTFFHIDGKGRRNKYDKKQAFVSVGDVHCSEKTRSSLSRILNIWEERGVYDKQQIASFRTAFNAALEPQTKRRKLSESNTEVLYDVDELETSASSDANIREKIAKLPPEVSEIQLLSKVQGKNITGQPDRVAAENLSIQVNEAVDLLTNYNTRLVTEMEDRKRASAMLKDYIaaqrelleqaeqrleVSETEIFLFLKKFDGEY
Disordered region (IsUnstruct)
*********************SIQTLSLWLIHHRKHHSTIVKTWIDEVEKADDHRKLTLMYLANDVIQNS****PEYGKEFGHVLKQAFVSVGDVHCSEKTRSSLSRILNIWEERGVYDKQQIASFRTAFNAAL*************TEVLYDVDGNVPIGYFTFFHIDGKGRRNKYDKKQAFVSVGDVHCSEKTRSSLSRILNIWEERGVYDKQQIASFRTAFNA******************************************************************VAAENLSIQVNEAVDLLTNYNTRLVTEM*******AMLKDYIAAQRELLEQAEQRLEVSETEIFLFLKKF****
Disordered Region (DISOPRED)
**GFTQSALISKLEELN***Q*IQTLSLWLIHHRKHHSTIVKTWIDEVEKADDHRKLTLMYLANDVIQNSKKKGPEYGKEFGHVLKQAFVSVGDVHCSEKTRSSLSRILNIWEERGVYDKQQIASFR*************************************************************************************************************LSESNTEVLYDVD**********************************************************LLTNYN******************************************FLFLKKF****
Disordered Region (DISEMBL)
MAGFTQSALISKLEELNASQQSIQTLSLWLIHHRKHHSTIVKTWIDEVEKADDHRKLTLMYLANDVIQNSKKKGPEYGKEFGHVLKQAFVSVGDVHCSEKTRSSLSRILNIWEERGVYDKQQIASFRTAFNAALEPQTKRRKLSESNTEVLYDVDGNVPIGYFTFFHIDGKGRRNKYDKKQAFVSVGDVHCSEKTRSSLSRILNIWEERGVYDKQQIASFRTAFNAALEPQTKRRKLSESNTEVLYDVDELETSASSDANIREKIAKLPPEVSEIQLLSKVQGKNITGQPDRVAAENLSIQVNEAVDLLTNYNTRLVTEMEDRKRASAMLKDYIAAQRELLEQAEQRLEVSETEIFLFLKKFDGEY
Disordered Region (DISPRO)
***FTQSALISKLEELNASQQSIQTLSLWLIHHRKHHSTIVKTWIDEVEKADDHRKLTLMYLANDVIQNSKKKGPEYGKEFGHVLKQAFVSVGDVHCSEKTRSSLSRILNIWEERGVYDKQQIASFRTAFNA****************EVLYDVDGNVPIGYFTFFHIDGKGRRNKYDKKQAFVSVGDVHCSEKTRSSLSRILNIWEERGVYDKQQIASFRTAFNAALEPQTKRRKLSESNTEVLYDVDELETSASSDANIREKIAKLPPE*S**QLLSK******T*QPDRVAAENLSIQVNEAVDLLTNYNTRLVTEMEDRKRASAMLKDYIAAQRELLEQAEQRLEVSETEIFLFLKKFDG*Y
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MAGFTQSALISKLEELNASQQSIQTLSLWLIHHRKHHSTIVKTWIDEVEKADDHRKLTLMYLANDVIQNSKKKGPEYGKEFGHVLKQAFVSVGDVHCSEKTRSSLSRILNIWEERGVYDKQQIASFRTAFNAALEPQTKRRKLSESNTEVLYDVDGNVPIGYFTFFHIDGKGRRNKYDKKQAFVSVGDVHCSEKTRSSLSRILNIWEERGVYDKQQIASFRTAFNAALEPQTKRRKLSESNTEVLYDVDELETSASSDANIREKIAKLPPEVSEIQLLSKVQGKNITGQPDRVAAENLSIQVNEAVDLLTNYNTRLVTEMEDRKRASAMLKDYxxxxxxxxxxxxxxxxxxxxxIFLFLKKFDGEY
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	366	2.2.26 [Sep-21-2011]
Q9CSU0	326	Regulation of nuclear pre	yes	N/A	0.439	0.493	0.457	6e-34
Q9NQG5	326	Regulation of nuclear pre	yes	N/A	0.439	0.493	0.457	6e-34
Q5R8Y3	312	Regulation of nuclear pre	no	N/A	0.377	0.442	0.496	4e-33
Q96P16	312	Regulation of nuclear pre	no	N/A	0.377	0.442	0.496	4e-33
Q0P5J9	312	Regulation of nuclear pre	no	N/A	0.377	0.442	0.496	4e-33
Q8VDS4	312	Regulation of nuclear pre	no	N/A	0.352	0.413	0.523	1e-32
Q5ZM30	268	Regulation of nuclear pre	no	N/A	0.352	0.481	0.523	2e-32
Q5VT52	1461	Regulation of nuclear pre	no	N/A	0.333	0.083	0.393	4e-17
Q6NXI6	1469	Regulation of nuclear pre	no	N/A	0.314	0.078	0.408	8e-17
A8WLG6	311	CID domain-containing pro	N/A	N/A	0.338	0.398	0.305	1e-14

>sp|Q9CSU0|RPR1B_MOUSE Regulation of nuclear pre-mRNA domain-containing protein 1B OS=Mus musculus GN=Rprd1b PE=1 SV=2

 Score =  145 bits (365), Expect = 6e-34,   Method: Compositional matrix adjust.
 Identities = 76/166 (45%), Positives = 101/166 (60%), Gaps = 5/166 (3%)

Query: 1   MAGFTQSALISKLEELNASQQSIQTLSLWLIHHRKHHSTIVKTWIDEVEKADDHRKLTLM 60
           M+ F++SAL  KL EL+ SQQS+QTLSLWLIHHRKH   IV  W  E+ KA  +RKLT +
Sbjct: 1   MSSFSESALEKKLSELSNSQQSVQTLSLWLIHHRKHAGPIVSVWHRELRKAKSNRKLTFL 60

Query: 61  YLANDVIQNSKKKGPEYGKEFGHVLKQAFVSVGDVHCSEKTRSSLSRILNIWEERGVYDK 120
           YLANDVIQNSK+KGPE+ +EF  VL  AF  V      E  +  L R+LNIW+ER VY  
Sbjct: 61  YLANDVIQNSKRKGPEFTREFESVLVDAFSHVAR-EADEGCKKPLERLLNIWQERSVYGG 119

Query: 121 QQIASFRTAFNAALEPQTK----RRKLSESNTEVLYDVDGNVPIGY 162
           + I   + +   +  P  K    ++ L  +  ++  + D + P  Y
Sbjct: 120 EFIQQLKLSMEDSKSPPPKAAEEKKSLKRTFQQIQEEEDDDYPGSY 165

Interacts with phosphorylated C-terminal heptapeptide repeat domain (CTD) of the largest RNA polymerase II subunit POLR2A, and participates in dephosphorylation of the CTD. Transcriptional regulator which enhances expression of CCND1. Promotes binding of RNA polymerase II to the CCDN1 promoter and to the termination region before the poly-A site but decreases its binding after the poly-A site. Prevents RNA polymerase II from reading through the 3' end termination site and may allow it to be recruited back to the promoter through promotion of the formation of a chromatin loop. Also enhances the transcription of a number of other cell cycle-related genes including CDK2, CDK4, CDK6 and cyclin-E but not CDKN1A, CDKN1B or cyclin-A. Promotes cell proliferation.
Mus musculus (taxid: 10090)

>sp|Q9NQG5|RPR1B_HUMAN Regulation of nuclear pre-mRNA domain-containing protein 1B OS=Homo sapiens GN=RPRD1B PE=1 SV=1

 Score =  145 bits (365), Expect = 6e-34,   Method: Compositional matrix adjust.
 Identities = 76/166 (45%), Positives = 101/166 (60%), Gaps = 5/166 (3%)

Query: 1   MAGFTQSALISKLEELNASQQSIQTLSLWLIHHRKHHSTIVKTWIDEVEKADDHRKLTLM 60
           M+ F++SAL  KL EL+ SQQS+QTLSLWLIHHRKH   IV  W  E+ KA  +RKLT +
Sbjct: 1   MSSFSESALEKKLSELSNSQQSVQTLSLWLIHHRKHAGPIVSVWHRELRKAKSNRKLTFL 60

Query: 61  YLANDVIQNSKKKGPEYGKEFGHVLKQAFVSVGDVHCSEKTRSSLSRILNIWEERGVYDK 120
           YLANDVIQNSK+KGPE+ +EF  VL  AF  V      E  +  L R+LNIW+ER VY  
Sbjct: 61  YLANDVIQNSKRKGPEFTREFESVLVDAFSHVAR-EADEGCKKPLERLLNIWQERSVYGG 119

Query: 121 QQIASFRTAFNAALEPQTK----RRKLSESNTEVLYDVDGNVPIGY 162
           + I   + +   +  P  K    ++ L  +  ++  + D + P  Y
Sbjct: 120 EFIQQLKLSMEDSKSPPPKATEEKKSLKRTFQQIQEEEDDDYPGSY 165

Interacts with phosphorylated C-terminal heptapeptide repeat domain (CTD) of the largest RNA polymerase II subunit POLR2A, and participates in dephosphorylation of the CTD. Transcriptional regulator which enhances expression of CCND1. Promotes binding of RNA polymerase II to the CCDN1 promoter and to the termination region before the poly-A site but decreases its binding after the poly-A site. Prevents RNA polymerase II from reading through the 3' end termination site and may allow it to be recruited back to the promoter through promotion of the formation of a chromatin loop. Also enhances the transcription of a number of other cell cycle-related genes including CDK2, CDK4, CDK6 and cyclin-E but not CDKN1A, CDKN1B or cyclin-A. Promotes cell proliferation.

Homo sapiens (taxid: 9606)

>sp|Q5R8Y3|RPR1A_PONAB Regulation of nuclear pre-mRNA domain-containing protein 1A OS=Pongo abelii GN=RPRD1A PE=2 SV=1

 Score =  142 bits (358), Expect = 4e-33,   Method: Compositional matrix adjust.
 Identities = 69/139 (49%), Positives = 92/139 (66%), Gaps = 1/139 (0%)

Query: 1   MAGFTQSALISKLEELNASQQSIQTLSLWLIHHRKHHSTIVKTWIDEVEKADDHRKLTLM 60
           M+ F+++AL  KL EL+ SQQS+QTLSLWLIHHRKH   IV  W  E+ KA  +RKLT +
Sbjct: 1   MSAFSEAALEKKLSELSNSQQSVQTLSLWLIHHRKHSRPIVTVWERELRKAKPNRKLTFL 60

Query: 61  YLANDVIQNSKKKGPEYGKEFGHVLKQAFVSVGDVHCSEKTRSSLSRILNIWEERGVYDK 120
           YLANDVIQNSK+KGPE+ K+F  V+ +AF  V      E  +  L R+L+IWEER VY+ 
Sbjct: 61  YLANDVIQNSKRKGPEFTKDFAPVIVEAFKHVSS-ETDESCKKHLGRVLSIWEERSVYEN 119

Query: 121 QQIASFRTAFNAALEPQTK 139
             +   + A     +P+ +
Sbjct: 120 DVLEQLKQALYGDKKPRKR 138

Interacts with phosphorylated C-terminal heptapeptide repeat domain (CTD) of the largest RNA polymerase II subunit POLR2A, and participates in dephosphorylation of the CTD. May act as a negative regulator of cyclin-D1 (CCND1) and cyclin-E (CCNE1) in the cell cycle.

Pongo abelii (taxid: 9601)

>sp|Q96P16|RPR1A_HUMAN Regulation of nuclear pre-mRNA domain-containing protein 1A OS=Homo sapiens GN=RPRD1A PE=1 SV=1

 Score =  142 bits (358), Expect = 4e-33,   Method: Compositional matrix adjust.
 Identities = 69/139 (49%), Positives = 92/139 (66%), Gaps = 1/139 (0%)

Query: 1   MAGFTQSALISKLEELNASQQSIQTLSLWLIHHRKHHSTIVKTWIDEVEKADDHRKLTLM 60
           M+ F+++AL  KL EL+ SQQS+QTLSLWLIHHRKH   IV  W  E+ KA  +RKLT +
Sbjct: 1   MSAFSEAALEKKLSELSNSQQSVQTLSLWLIHHRKHSRPIVTVWERELRKAKPNRKLTFL 60

Query: 61  YLANDVIQNSKKKGPEYGKEFGHVLKQAFVSVGDVHCSEKTRSSLSRILNIWEERGVYDK 120
           YLANDVIQNSK+KGPE+ K+F  V+ +AF  V      E  +  L R+L+IWEER VY+ 
Sbjct: 61  YLANDVIQNSKRKGPEFTKDFAPVIVEAFKHVSS-ETDESCKKHLGRVLSIWEERSVYEN 119

Query: 121 QQIASFRTAFNAALEPQTK 139
             +   + A     +P+ +
Sbjct: 120 DVLEQLKQALYGDKKPRKR 138

Interacts with phosphorylated C-terminal heptapeptide repeat domain (CTD) of the largest RNA polymerase II subunit POLR2A, and participates in dephosphorylation of the CTD. May act as a negative regulator of cyclin-D1 (CCND1) and cyclin-E (CCNE1) in the cell cycle.

Homo sapiens (taxid: 9606)

>sp|Q0P5J9|RPR1A_BOVIN Regulation of nuclear pre-mRNA domain-containing protein 1A OS=Bos taurus GN=RPRD1A PE=2 SV=2

 Score =  142 bits (358), Expect = 4e-33,   Method: Compositional matrix adjust.
 Identities = 69/139 (49%), Positives = 92/139 (66%), Gaps = 1/139 (0%)

Query: 1   MAGFTQSALISKLEELNASQQSIQTLSLWLIHHRKHHSTIVKTWIDEVEKADDHRKLTLM 60
           M+ F+++AL  KL EL+ SQQS+QTLSLWLIHHRKH   IV  W  E+ KA  +RKLT +
Sbjct: 1   MSAFSEAALEKKLSELSNSQQSVQTLSLWLIHHRKHSRPIVTVWERELRKAKPNRKLTFL 60

Query: 61  YLANDVIQNSKKKGPEYGKEFGHVLKQAFVSVGDVHCSEKTRSSLSRILNIWEERGVYDK 120
           YLANDVIQNSK+KGPE+ K+F  V+ +AF  V      E  +  L R+L+IWEER VY+ 
Sbjct: 61  YLANDVIQNSKRKGPEFTKDFAPVIVEAFKHVSS-ETDESCKKHLGRVLSIWEERSVYEN 119

Query: 121 QQIASFRTAFNAALEPQTK 139
             +   + A     +P+ +
Sbjct: 120 DVLEQLKQALYGDKKPRKR 138

Interacts with phosphorylated C-terminal heptapeptide repeat domain (CTD) of the largest RNA polymerase II subunit POLR2A, and participates in dephosphorylation of the CTD. May act as a negative regulator of cyclin-D1 (CCND1) and cyclin-E (CCNE1) in the cell cycle.

Bos taurus (taxid: 9913)

>sp|Q8VDS4|RPR1A_MOUSE Regulation of nuclear pre-mRNA domain-containing protein 1A OS=Mus musculus GN=Rprd1a PE=2 SV=1

 Score =  140 bits (354), Expect = 1e-32,   Method: Compositional matrix adjust.
 Identities = 68/130 (52%), Positives = 88/130 (67%), Gaps = 1/130 (0%)

Query: 1   MAGFTQSALISKLEELNASQQSIQTLSLWLIHHRKHHSTIVKTWIDEVEKADDHRKLTLM 60
           M+ F+++AL  KL EL+ SQQS+QTLSLWLIHHRKH   IV  W  E+ KA  +RKLT +
Sbjct: 1   MSAFSEAALEKKLSELSNSQQSVQTLSLWLIHHRKHSRPIVTVWERELRKAKPNRKLTFL 60

Query: 61  YLANDVIQNSKKKGPEYGKEFGHVLKQAFVSVGDVHCSEKTRSSLSRILNIWEERGVYDK 120
           YLANDVIQNSK+KGPE+ K+F  V+ +AF  V      E  +  L R+L+IWEER VY+ 
Sbjct: 61  YLANDVIQNSKRKGPEFTKDFAPVIVEAFKHVSS-ETDESCKKHLGRVLSIWEERSVYEN 119

Query: 121 QQIASFRTAF 130
             +   + A 
Sbjct: 120 DVLEQLKHAL 129

Interacts with phosphorylated C-terminal heptapeptide repeat domain (CTD) of the largest RNA polymerase II subunit POLR2A, and participates in dephosphorylation of the CTD. May act as a negative regulator of cyclin-D1 (CCND1) and cyclin-E (CCNE1) in the cell cycle.

Mus musculus (taxid: 10090)

>sp|Q5ZM30|RPR1A_CHICK Regulation of nuclear pre-mRNA domain-containing protein 1A OS=Gallus gallus GN=RPRD1A PE=2 SV=1

 Score =  140 bits (353), Expect = 2e-32,   Method: Compositional matrix adjust.
 Identities = 68/130 (52%), Positives = 88/130 (67%), Gaps = 1/130 (0%)

Query: 1   MAGFTQSALISKLEELNASQQSIQTLSLWLIHHRKHHSTIVKTWIDEVEKADDHRKLTLM 60
           M+ F+++AL  KL EL+ SQQS+QTLSLWLIHHRKH + IV  W  E+ KA  +RKLT +
Sbjct: 1   MSAFSEAALERKLSELSNSQQSVQTLSLWLIHHRKHSALIVSVWERELRKAKPNRKLTFL 60

Query: 61  YLANDVIQNSKKKGPEYGKEFGHVLKQAFVSVGDVHCSEKTRSSLSRILNIWEERGVYDK 120
           YLANDVIQNSK+KGPE+ K+F  V+ +AF  V      E  +    R+L+IWEER VY+ 
Sbjct: 61  YLANDVIQNSKRKGPEFTKDFAPVIVEAFKHVSS-ESDESCKKHPGRVLSIWEERSVYEN 119

Query: 121 QQIASFRTAF 130
             +   R A 
Sbjct: 120 DVLEQLRQAL 129

Gallus gallus (taxid: 9031)

>sp|Q5VT52|RPRD2_HUMAN Regulation of nuclear pre-mRNA domain-containing protein 2 OS=Homo sapiens GN=RPRD2 PE=1 SV=1

 Score = 89.4 bits (220), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 50/127 (39%), Positives = 72/127 (56%), Gaps = 5/127 (3%)

Query: 12  KLEELNASQQSIQTLSLWLIHHRKHHSTIVKTWIDEVEKADDHRKLTLMYLANDVIQNSK 71
           K + +  + +SIQ LS W I ++KHHSTIV  W+  + ++    +L L YLANDVIQN K
Sbjct: 30  KFQSVTNTMESIQGLSSWCIENKKHHSTIVYHWMKWLRRSAYPHRLNLFYLANDVIQNCK 89

Query: 72  KKGPEYGKE-FGHVLKQAFVSVGDVHCSEKTRSSLSRILNIWEERGVYDKQQIASFRTAF 130
           +K     +E F  VL +A   V D   S+    S+ RI  IWE+R VY ++ I + R A 
Sbjct: 90  RKNAIIFRESFADVLPEAAALVKDPSVSK----SVERIFKIWEDRNVYPEEMIVALREAL 145

Query: 131 NAALEPQ 137
           +   + Q
Sbjct: 146 STTFKTQ 152

Homo sapiens (taxid: 9606)

>sp|Q6NXI6|RPRD2_MOUSE Regulation of nuclear pre-mRNA domain-containing protein 2 OS=Mus musculus GN=Rprd2 PE=1 SV=1

 Score = 88.6 bits (218), Expect = 8e-17,   Method: Compositional matrix adjust.
 Identities = 49/120 (40%), Positives = 68/120 (56%), Gaps = 5/120 (4%)

Query: 12  KLEELNASQQSIQTLSLWLIHHRKHHSTIVKTWIDEVEKADDHRKLTLMYLANDVIQNSK 71
           K + +  + +SIQ LS W I ++KHHSTIV  W+  + ++    +L L YLANDVIQN K
Sbjct: 30  KFQSVTNTMESIQGLSSWCIENKKHHSTIVYHWMKWLRRSTYPHRLNLFYLANDVIQNCK 89

Query: 72  KKGPEYGKE-FGHVLKQAFVSVGDVHCSEKTRSSLSRILNIWEERGVYDKQQIASFRTAF 130
           +K     +E F  VL +A   V D   S+    S+ RI  IWE+R VY +  I + R A 
Sbjct: 90  RKNAIIFRESFADVLPEAAALVKDPSVSK----SIERIFKIWEDRNVYPEDMIVALREAL 145

Mus musculus (taxid: 10090)

>sp|A8WLG6|CIDS1_CAEBR CID domain-containing protein 1 OS=Caenorhabditis briggsae GN=cids-1 PE=4 SV=1

 Score = 80.9 bits (198), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 41/134 (30%), Positives = 74/134 (55%), Gaps = 10/134 (7%)

Query: 1   MAGFTQSALISKLEELNASQQSIQTLSLWLIHHRKHHSTIVKTWIDEVEKADDHRKLT-L 59
           M+ FT+  L  KL  L+    SIQT S WL+ +  +   I++ W+  V K +   K+  L
Sbjct: 1   MSDFTEQTLRQKLANLSNHSNSIQTTSSWLLKNHNNREIIIRVWLKTVRKENKGAKVVNL 60

Query: 60  MYLANDVIQNSKKKGPEYGKEFGHVLKQAFVSVGDVHCSE----KTRSSLSRILNIWEER 115
           +Y+ANDV QN++K  P++  +F   ++ AF      HC E    +  +++ +++++W+ER
Sbjct: 61  LYVANDVAQNARKACPQFKDDFFPAIESAF-----RHCCELKAKEVENAIGKLIHVWKER 115

Query: 116 GVYDKQQIASFRTA 129
            +Y + Q    + A
Sbjct: 116 QIYSQSQCKRLQEA 129

Caenorhabditis briggsae (taxid: 6238)

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	366
289741593	308	regulator of nuclear mRNA [Glossina mors	0.797	0.948	0.446	1e-68
193610549	346	PREDICTED: regulation of nuclear pre-mRN	0.781	0.826	0.430	6e-68
195016756	386	GH16483 [Drosophila grimshawi] gi|193897	0.887	0.841	0.430	3e-66
157108809	356	hypothetical protein AaeL_AAEL005103 [Ae	0.836	0.859	0.426	7e-64
312372605	481	hypothetical protein AND_19932 [Anophele	0.825	0.627	0.441	1e-63
157108953	356	hypothetical protein AaeL_AAEL005158 [Ae	0.836	0.859	0.424	1e-63
427786899	351	Putative regulation of nuclear pre-mrna	0.803	0.837	0.434	1e-61
350412493	338	PREDICTED: regulation of nuclear pre-mRN	0.743	0.804	0.437	4e-60
328779153	338	PREDICTED: regulation of nuclear pre-mRN	0.743	0.804	0.437	4e-60
158294003	355	AGAP005331-PA [Anopheles gambiae str. PE	0.786	0.811	0.417	6e-58

>gi|289741593|gb|ADD19544.1| regulator of nuclear mRNA [Glossina morsitans morsitans]

 Score =  266 bits (679), Expect = 1e-68,   Method: Compositional matrix adjust.
 Identities = 156/349 (44%), Positives = 212/349 (60%), Gaps = 57/349 (16%)

Query: 1   MAGFTQSALISKLEELNASQQSIQTLSLWLIHHRKHHSTIVKTWIDEVEKADDHRKLTLM 60
           M+ FT++AL+ KL ELN+SQQSIQTLSLWLIHHRKHH+ I+KTW+ E+E   + +KL  M
Sbjct: 1   MSAFTETALLKKLAELNSSQQSIQTLSLWLIHHRKHHAGIIKTWLREIENVPESKKLIFM 60

Query: 61  YLANDVIQNSKKKGPEYGKEFGHVLKQAFVSVGDVHCSEKTRSSLSRILNIWEERGVYDK 120
           YLANDVIQNSKKKGPEYGKEF ++L + F  +G+   S+K   +L RILNIWEERGVY+ 
Sbjct: 61  YLANDVIQNSKKKGPEYGKEFSNILPKVFSHIGETCTSDKLFGNLGRILNIWEERGVYEP 120

Query: 121 QQIASFRTAFNAALEPQTKRRKLSESNTEVLYDVDGNVPIGYFTFFHIDGKGRRNKYDKK 180
           + IA FR   N          K ++SN       +GN           DGK R+N+ + K
Sbjct: 121 KMIADFRAKLN----------KQNQSN-------EGN-----------DGK-RKNEENNK 151

Query: 181 QAFVSVGDVHCSEKTRSSLSRILNIWEERGVYDKQQIASFRTAFNAALEPQTKRRKLSES 240
                      S+   ++L   LN   E+  Y                EP+         
Sbjct: 152 TKVKRSRTSSDSDDKNTALLFELNGDAEQSPY---------LPLGDPPEPE--------- 193

Query: 241 NTEVLYDVDELETSASSDANIREKIAKLPPEVSEIQLLSKVQGKNITGQPDRVAAENLSI 300
             E++  + ++E SASSDA +RE+IA LPPE+SEI  L+K++        D+ AA+ L+ 
Sbjct: 194 --ELIKALVKIENSASSDAIVRERIANLPPEISEISCLNKLE--------DKDAAKALAN 243

Query: 301 QVNEAVDLLTNYNTRLVTEMEDRKRASAMLKDYIAAQRELLEQAEQRLE 349
           QVNEAV+LL +YN+RL  EME+R + ++ML+D+ A Q+ELL QAE+RLE
Sbjct: 244 QVNEAVELLNDYNSRLAAEMEERTKLASMLRDFQAEQKELLVQAEKRLE 292

Source: Glossina morsitans morsitans

Species: Glossina morsitans

Genus: Glossina

Family: Glossinidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|193610549|ref|XP_001946035.1| PREDICTED: regulation of nuclear pre-mRNA domain-containing protein 1B-like [Acyrthosiphon pisum]

 Score =  264 bits (674), Expect = 6e-68,   Method: Compositional matrix adjust.
 Identities = 154/358 (43%), Positives = 209/358 (58%), Gaps = 72/358 (20%)

Query: 1   MAGFTQSALISKLEELNASQQSIQTLSLWLIHHRKHHSTIVKTWIDEVEKADDHRKLTLM 60
           M GFT+ +L S+L++LN+SQQSIQTLSLWLIHHRK+  T+VK W  E+    + ++LTLM
Sbjct: 1   MTGFTEGSLNSRLKDLNSSQQSIQTLSLWLIHHRKYAHTVVKIWSREILAGSESKQLTLM 60

Query: 61  YLANDVIQNSKKKGPEYGKEFGHVLKQAFVSVGDVHCSEKTRSSLSRILNIWEERGVYDK 120
           YLAND+IQN KKKGPEYGKEFG  L +AF  +   +CS KTR SL+R+LNIWEERGVY K
Sbjct: 61  YLANDIIQNGKKKGPEYGKEFGKELAKAFKQISLNNCSSKTRQSLTRLLNIWEERGVYSK 120

Query: 121 QQIASFRTAFN------AALEPQTKRRKLSESNTEVLYDVDGNVPIGYFTFFHIDGKGRR 174
            QI  F+ AF          EP +K+ K S +                            
Sbjct: 121 IQIDEFKDAFGKESAKKPTGEPPSKKVKHSHN---------------------------- 152

Query: 175 NKYDKKQAFVSVGDVHCSEKTRSSLSRILN----IWEERGVYDKQQIASFRTAFNAALEP 230
                          H S+KT+S  + I      I E  G  +     S +T  N   EP
Sbjct: 153 ---------------HKSKKTKSQNNGIKKDKEVIVEVDGAKELHVTLSPKTPVNDPPEP 197

Query: 231 QTKRRKLSESNTEVLYDVDELETSASSDANIREKIAKLPPEVSEIQLLSKVQGKNITGQP 290
           +           E++  +++LE + S DA +RE+I+KLPPE++++ LLS+++GK+     
Sbjct: 198 E-----------ELIKALNDLENAPSCDAVVRERISKLPPEIADVSLLSQLKGKD----- 241

Query: 291 DRVAAENLSIQVNEAVDLLTNYNTRLVTEMEDRKRASAMLKDYIAAQRELLEQAEQRL 348
                E L  +VN+AV LLT+YNTRLV EMEDRK+  +ML D+I +QR+L++QAEQRL
Sbjct: 242 ---EGEELLRKVNDAVALLTDYNTRLVCEMEDRKKVFSMLHDFIQSQRDLIDQAEQRL 296

Source: Acyrthosiphon pisum

Species: Acyrthosiphon pisum

Genus: Acyrthosiphon

Family: Aphididae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195016756|ref|XP_001984478.1| GH16483 [Drosophila grimshawi] gi|193897960|gb|EDV96826.1| GH16483 [Drosophila grimshawi]

 Score =  258 bits (660), Expect = 3e-66,   Method: Compositional matrix adjust.
 Identities = 155/360 (43%), Positives = 210/360 (58%), Gaps = 35/360 (9%)

Query: 1   MAGFTQSALISKLEELNASQQSIQTLSLWLIHHRKHHSTIVKTWIDEVEKADDHRKLTLM 60
           M+ FT+SAL+ KL ELN SQQSIQTLSLWLIHHRKHH+ IV+TW  E++   + +KLT M
Sbjct: 1   MSAFTESALLKKLSELNPSQQSIQTLSLWLIHHRKHHTVIVQTWQRELQNVPEPKKLTFM 60

Query: 61  YLANDVIQNSKKKGPEYGKEFGHVLKQAFVSVGDVHCSEKTRSSLSRILNIWEERGVYDK 120
           YLANDVIQNSKKKGPEYGKEFG+VL + F  +G+   SEK   SL RILNIW+ERGVYD 
Sbjct: 61  YLANDVIQNSKKKGPEYGKEFGNVLPKVFAHIGETCSSEKLLGSLGRILNIWQERGVYDP 120

Query: 121 QQIASFRTAFNAALEPQTKRRKLSESNTEVLYDVDGNVPIGYFTFFHIDGKGRRNKYDKK 180
           + I  +             R +++    +   + +GN         + + KG        
Sbjct: 121 KTIVDY-------------RARMNSEAKDAPANANGNGSSSSTKTSNSNSKGATVSAVPH 167

Query: 181 QAFVSVGDVHCSEKTRSSLSRILNIWEERGVYDKQQIASFRTAFNAALEPQTKRRKLSES 240
           ++  +      SEK+     R     EER    K+  AS      + +EP     +   +
Sbjct: 168 KSSSNSNSGSKSEKSEKREKRK---HEERQSKSKRPRASSHHQSVSVVEPPAPEAENGHT 224

Query: 241 NT-----------EVLYDVDELETSASSDANIREKIAKLPPEVSEIQLLSKVQGKNITGQ 289
                        E++  +  +E SASSDA +RE+IAKLPPE+SEI  ++K++       
Sbjct: 225 PPYLTLGEPPEPEELIKALTSIENSASSDALVRERIAKLPPEISEIGCITKLE------- 277

Query: 290 PDRVAAENLSIQVNEAVDLLTNYNTRLVTEMEDRKRASAMLKDYIAAQRELLEQAEQRLE 349
            D+  A+ L+ QVNEAVDLL +YN RL  EME+R + +AML+D+ A Q+ELL QAE RL+
Sbjct: 278 -DKDKAKVLAKQVNEAVDLLNDYNARLSAEMEERTKLAAMLRDFQAEQKELLAQAELRLD 336

Source: Drosophila grimshawi

Species: Drosophila grimshawi

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|157108809|ref|XP_001650398.1| hypothetical protein AaeL_AAEL005103 [Aedes aegypti] gi|108879240|gb|EAT43465.1| AAEL005103-PA [Aedes aegypti]

 Score =  250 bits (639), Expect = 7e-64,   Method: Compositional matrix adjust.
 Identities = 149/349 (42%), Positives = 199/349 (57%), Gaps = 43/349 (12%)

Query: 1   MAGFTQSALISKLEELNASQQSIQTLSLWLIHHRKHHSTIVKTWIDEVEKADDHRKLTLM 60
           M+ FT+S L+ KL ELN SQQSIQTLSLWLIHHRKHHS IV+TW+ E++KA   +KLT M
Sbjct: 1   MSSFTESGLVKKLLELNPSQQSIQTLSLWLIHHRKHHSIIVRTWLKELQKAPTSKKLTFM 60

Query: 61  YLANDVIQNSKKKGPEYGKEFGHVLKQAFVSVGDVHCSEKTRSSLSRILNIWEERGVYDK 120
           YLANDVIQNSKKKGPE+GKEF +VL +AF  +      EKT  +L+RIL+IW ERGVY++
Sbjct: 61  YLANDVIQNSKKKGPEFGKEFENVLLKAFKVIAQSGPEEKTIHNLNRILHIWGERGVYEE 120

Query: 121 QQIASFRTAFNAALEPQTKRRKLSESNTEVLYDVDGNVPIGYFTFFHIDGKGRRNKYDKK 180
            +I  F  A N   +     + + E       D                  G    +++K
Sbjct: 121 AKIKEFSGALNQREKSPAAPKAVVEEKKRKAED------------------GHEPSHNQK 162

Query: 181 QAFVSVGDVHCSEKTRSSLSRILNIWEERGVYDKQQIASFRTAFNAALEPQTKRRKLSES 240
           +A  S       +K +S    +    E        Q           +            
Sbjct: 163 KAKSSEKSHSAEKKAKSETIEVNGTVETHVTLSPHQPEGDPPEPEELI------------ 210

Query: 241 NTEVLYDVDELETSASSDANIREKIAKLPPEVSEIQLLSKVQGKNITGQPDRVAAENLSI 300
             +VL D   LE SASSDA +RE+IA LPPEVSE+  L+K++        D+ AA  L++
Sbjct: 211 --KVLQD---LENSASSDAVVRERIANLPPEVSELSALAKLE--------DKEAANRLAL 257

Query: 301 QVNEAVDLLTNYNTRLVTEMEDRKRASAMLKDYIAAQRELLEQAEQRLE 349
           +VN+A+ +L +YN RL TEM+DRK+ + MLKD+   Q+ELL QAEQRL+
Sbjct: 258 KVNDAIKILNDYNARLATEMDDRKKLTTMLKDFQREQQELLVQAEQRLQ 306

Source: Aedes aegypti

Species: Aedes aegypti

Genus: Aedes

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|312372605|gb|EFR20532.1| hypothetical protein AND_19932 [Anopheles darlingi]

 Score =  249 bits (637), Expect = 1e-63,   Method: Compositional matrix adjust.
 Identities = 156/353 (44%), Positives = 206/353 (58%), Gaps = 51/353 (14%)

Query: 1   MAGFTQSALISKLEELNASQQSIQTLSLWLIHHRKHHSTIVKTWIDEVEKADDHRKLTLM 60
           M+ FT++ L+ KL +LN+SQQSIQTLSLWLIHHRKHHS IVKTW+ E+ KA   +KLT M
Sbjct: 126 MSSFTETGLVKKLLDLNSSQQSIQTLSLWLIHHRKHHSIIVKTWLKELAKAPAAKKLTFM 185

Query: 61  YLANDVIQNSKKKGPEYGKEFGHVLKQAFVSVGDVHCSEKTRSSLSRILNIWEERGVYDK 120
           YLANDVIQNSKKKGPE+G+EF HVL +AF  +       KT +SL+RILNIW ERGVY++
Sbjct: 186 YLANDVIQNSKKKGPEFGREFEHVLLKAFRYIAQSSPEPKTINSLNRILNIWGERGVYEE 245

Query: 121 QQIASFRTAFN----AALEPQTKRRKLSESNTEVLYDVDGNVPIGYFTFFHIDGKGRRNK 176
            +I  +  A N    A +EP     K  +  T VL DV         T            
Sbjct: 246 PKIKEYSAALNEGETARVEPVNGSEKKRKPET-VLSDV--------LT------------ 284

Query: 177 YDKKQAFVSVGDVHCSEKTRSSLSRILNIWEERGVYDKQQIASFRTAFNAALEPQTKRRK 236
              K+A  +VG +   +K +S       + E  G  +     S         EP+     
Sbjct: 285 ESNKKARPTVG-ITVEKKAKSE------VVEVNGKVETHITLSPHQPDGDPPEPE----- 332

Query: 237 LSESNTEVLYDVDELETSASSDANIREKIAKLPPEVSEIQLLSKVQGKNITGQPDRVAAE 296
                 E++  + ELE SASSDA +RE+IA L PEVSE+  ++K++        D+ AA 
Sbjct: 333 ------ELIKVILELENSASSDAVVRERIANLKPEVSELAAINKLE--------DKEAAI 378

Query: 297 NLSIQVNEAVDLLTNYNTRLVTEMEDRKRASAMLKDYIAAQRELLEQAEQRLE 349
            L+  VN+A+ +L +YN RL TEMEDRK+ + ML+D+   Q+ELL QAE RLE
Sbjct: 379 KLATDVNDAIKILNDYNARLATEMEDRKKLTTMLRDFQREQQELLLQAENRLE 431

Source: Anopheles darlingi

Species: Anopheles darlingi

Genus: Anopheles

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|157108953|ref|XP_001650459.1| hypothetical protein AaeL_AAEL005158 [Aedes aegypti] gi|108879180|gb|EAT43405.1| AAEL005158-PA [Aedes aegypti]

 Score =  249 bits (636), Expect = 1e-63,   Method: Compositional matrix adjust.
 Identities = 148/349 (42%), Positives = 199/349 (57%), Gaps = 43/349 (12%)

Query: 1   MAGFTQSALISKLEELNASQQSIQTLSLWLIHHRKHHSTIVKTWIDEVEKADDHRKLTLM 60
           M+ FT+S L+ KL ELN SQQSIQTLSLWLIHHRKHHS IV+TW+ E++KA   +KLT M
Sbjct: 1   MSSFTESGLVKKLLELNPSQQSIQTLSLWLIHHRKHHSIIVRTWLKELQKAPTSKKLTFM 60

Query: 61  YLANDVIQNSKKKGPEYGKEFGHVLKQAFVSVGDVHCSEKTRSSLSRILNIWEERGVYDK 120
           YLANDVIQNSKKKGPE+GKEF +VL +AF  +      EKT  +++RIL+IW ERGVY++
Sbjct: 61  YLANDVIQNSKKKGPEFGKEFENVLLKAFKVIAQSGPEEKTIHNINRILHIWGERGVYEE 120

Query: 121 QQIASFRTAFNAALEPQTKRRKLSESNTEVLYDVDGNVPIGYFTFFHIDGKGRRNKYDKK 180
            +I  F  A N   +     + + E       D                  G    +++K
Sbjct: 121 AKIKEFSGALNQREKSPAAPKAVVEEKKRKAED------------------GHEPSHNQK 162

Query: 181 QAFVSVGDVHCSEKTRSSLSRILNIWEERGVYDKQQIASFRTAFNAALEPQTKRRKLSES 240
           +A  S       +K +S    +    E        Q           +            
Sbjct: 163 KAKSSEKSHSAEKKAKSETIEVNGTVETHVTLSPHQPEGDPPEPEELI------------ 210

Query: 241 NTEVLYDVDELETSASSDANIREKIAKLPPEVSEIQLLSKVQGKNITGQPDRVAAENLSI 300
             +VL D   LE SASSDA +RE+IA LPPEVSE+  L+K++        D+ AA  L++
Sbjct: 211 --KVLQD---LENSASSDAVVRERIANLPPEVSELSALAKLE--------DKEAANRLAL 257

Query: 301 QVNEAVDLLTNYNTRLVTEMEDRKRASAMLKDYIAAQRELLEQAEQRLE 349
           +VN+A+ +L +YN RL TEM+DRK+ + MLKD+   Q+ELL QAEQRL+
Sbjct: 258 KVNDAIKILNDYNARLATEMDDRKKLTTMLKDFQREQQELLVQAEQRLQ 306

Source: Aedes aegypti

Species: Aedes aegypti

Genus: Aedes

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|427786899|gb|JAA58901.1| Putative regulation of nuclear pre-mrna domain-containing protein 1b [Rhipicephalus pulchellus]

 Score =  243 bits (619), Expect = 1e-61,   Method: Compositional matrix adjust.
 Identities = 155/357 (43%), Positives = 197/357 (55%), Gaps = 63/357 (17%)

Query: 1   MAGFTQSALISKLEELNASQQSIQTLSLWLIHHRKHHSTIVKTWIDEVEKADDHRKLTLM 60
           M+GFT++AL  KL ELN SQQSIQTLSLWLIHHRKHH TIV  W+ E++KA   RKLT M
Sbjct: 1   MSGFTEAALERKLAELNNSQQSIQTLSLWLIHHRKHHKTIVHVWLRELKKAKPARKLTFM 60

Query: 61  YLANDVIQNSKKKGPEYGKEFGHVLKQAFVSVGDVHCSEKTRSSLSRILNIWEERGVYDK 120
           YLANDVIQNSKKKGPE+ KEF  VL +AF  +      +KT + L RIL++W+ER V+D 
Sbjct: 61  YLANDVIQNSKKKGPEFTKEFATVLAKAFAHISVRDTDQKTHAGLRRILSVWKERSVFDS 120

Query: 121 QQIASFRTAFNAALEPQTKRRKLSESNTEVLYDVDGNVPIGYFTFFHIDGKGRRNKYDKK 180
            QI+ F          Q    K+SE  T                   +   G+   Y K 
Sbjct: 121 HQISDFG---------QYLSDKVSEPET-------------------VKDSGQDAAYRKG 152

Query: 181 QAFVSVGDVHCSEKTRSSLSRILNIWEERGVYDKQQIASFRTAFNAALEP--QTKRRKLS 238
            A VS       E T         +W      D +  A  +   +   EP  +T   K +
Sbjct: 153 HAPVS------HEGT--------PLWN-----DAEPAAKRKKPSDPGDEPSEKTDAAKDA 193

Query: 239 ESNTE------VLYDVDELETSASSDANIREKIAKLPPEVSEIQLLSKVQGKNITGQPDR 292
           E   E      ++  + +LE +ASSDA +RE+IA LPPEVS+  LL K+Q        DR
Sbjct: 194 EKPGEPPDPGVLIKALADLENTASSDAVVRERIASLPPEVSDASLLEKIQ--------DR 245

Query: 293 VAAENLSIQVNEAVDLLTNYNTRLVTEMEDRKRASAMLKDYIAAQRELLEQAEQRLE 349
            AA+ LS+QV EA  LL  YN+RL  E+EDRK+ S ML  +   QREL+  AEQ+LE
Sbjct: 246 QAADRLSVQVEEACSLLAEYNSRLAQELEDRKQVSQMLASFTFHQRELMALAEQKLE 302

Source: Rhipicephalus pulchellus

Species: Rhipicephalus pulchellus

Genus: Rhipicephalus

Family: Ixodidae

Order: Ixodida

Class: Arachnida

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|350412493|ref|XP_003489666.1| PREDICTED: regulation of nuclear pre-mRNA domain-containing protein 1B-like [Bombus impatiens]

 Score =  238 bits (606), Expect = 4e-60,   Method: Compositional matrix adjust.
 Identities = 146/334 (43%), Positives = 181/334 (54%), Gaps = 62/334 (18%)

Query: 1   MAGFTQSALISKLEELNASQQSIQTLSLWLIHHRKHHSTIVKTWIDEVEKADDHRKLTLM 60
           M GFT+SAL+ +L +LN SQQSIQTLSLWLIHHRKHH TIVK W  E+ K  D+RKL  M
Sbjct: 1   MTGFTESALVKRLMDLNPSQQSIQTLSLWLIHHRKHHPTIVKVWFKEMCKVKDNRKLMFM 60

Query: 61  YLANDVIQNSKKKGPEYGKEFGHVLKQAFVSVGDVHCSEKTRSSLSRILNIWEERGVYDK 120
           YLANDVIQNSKKKGPE+GKEF  VL +AF  +      EKTR  L+R+L IWEERGVYDK
Sbjct: 61  YLANDVIQNSKKKGPEFGKEFETVLPKAFEHMKGF--DEKTRERLNRLLQIWEERGVYDK 118

Query: 121 QQIASFRTAF-NAALEPQTKRRKLSESNTEVLYDVDGNVPIGYFTFFHIDGKGRRNKYDK 179
            QIA F+ AF + + +P T   K    N       D        T   +DG         
Sbjct: 119 AQIAEFKAAFTDTSKDPGTPPPKKKFKNDIEKIKKDKKERKKSETEVEVDG--------- 169

Query: 180 KQAFVSVGDVHCSEKTRSSLSRILNIWEERGVYDKQQIASFRTAFNAALEPQTKRRKLSE 239
                   ++H +   R+                            A   P+T      E
Sbjct: 170 ------TKELHVTLSPRTP---------------------------AGDPPET------E 190

Query: 240 SNTEVLYDVDELETSASSDANIREKIAKLPPEVSEIQLLSKVQGKNITGQPDRVAAENLS 299
              + L D++   +S   DA +RE+IA LPPEVSE+ LL+ +         DR AA+ LS
Sbjct: 191 ELIKALMDLENTASS---DAGVRERIASLPPEVSEVSLLANLA--------DRAAADQLS 239

Query: 300 IQVNEAVDLLTNYNTRLVTEMEDRKRASAMLKDY 333
           + VNEA  LL +YN RL  EMEDR+R   ML+DY
Sbjct: 240 VAVNEAAALLADYNGRLQAEMEDRRRLLTMLRDY 273

Source: Bombus impatiens

Species: Bombus impatiens

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|328779153|ref|XP_396379.4| PREDICTED: regulation of nuclear pre-mRNA domain-containing protein 1B-like [Apis mellifera]

 Score =  238 bits (606), Expect = 4e-60,   Method: Compositional matrix adjust.
 Identities = 146/334 (43%), Positives = 181/334 (54%), Gaps = 62/334 (18%)

Query: 1   MAGFTQSALISKLEELNASQQSIQTLSLWLIHHRKHHSTIVKTWIDEVEKADDHRKLTLM 60
           M GFT+SAL+ +L +LN SQQSIQTLSLWLIHHRKHH TIVK W  E+ K  D+RKL  M
Sbjct: 1   MTGFTESALVKRLMDLNPSQQSIQTLSLWLIHHRKHHPTIVKVWFKEMCKVKDNRKLMFM 60

Query: 61  YLANDVIQNSKKKGPEYGKEFGHVLKQAFVSVGDVHCSEKTRSSLSRILNIWEERGVYDK 120
           YLANDVIQNSKKKGPE+GKEF  VL +AF  +      EKTR  L+R+L IWEERGVYDK
Sbjct: 61  YLANDVIQNSKKKGPEFGKEFETVLPKAFEHMKGF--DEKTRERLNRLLQIWEERGVYDK 118

Query: 121 QQIASFRTAF-NAALEPQTKRRKLSESNTEVLYDVDGNVPIGYFTFFHIDGKGRRNKYDK 179
            QIA F+ AF + + +P T   K    N       D        T   +DG         
Sbjct: 119 TQIAEFKAAFTDTSRDPGTPPPKKKLKNDIEKVKKDKKERKKSETEVEVDG--------- 169

Query: 180 KQAFVSVGDVHCSEKTRSSLSRILNIWEERGVYDKQQIASFRTAFNAALEPQTKRRKLSE 239
                   ++H +   R+                            A   P+T      E
Sbjct: 170 ------TKELHVTLSPRTP---------------------------AGDPPET------E 190

Query: 240 SNTEVLYDVDELETSASSDANIREKIAKLPPEVSEIQLLSKVQGKNITGQPDRVAAENLS 299
              + L D++   +S   DA +RE+IA LPPEVSE+ LL+ +         DR AA+ LS
Sbjct: 191 ELIKALMDLENTASS---DAGVRERIASLPPEVSEVSLLANLA--------DRAAADQLS 239

Query: 300 IQVNEAVDLLTNYNTRLVTEMEDRKRASAMLKDY 333
           + VNEA  LL +YN RL  EMEDR+R   ML+DY
Sbjct: 240 VAVNEAAALLADYNGRLQAEMEDRRRLLTMLRDY 273

Source: Apis mellifera

Species: Apis mellifera

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|158294003|ref|XP_555972.2| AGAP005331-PA [Anopheles gambiae str. PEST] gi|157015363|gb|EAL39798.2| AGAP005331-PA [Anopheles gambiae str. PEST]

 Score =  230 bits (587), Expect = 6e-58,   Method: Compositional matrix adjust.
 Identities = 140/335 (41%), Positives = 191/335 (57%), Gaps = 47/335 (14%)

Query: 1   MAGFTQSALISKLEELNASQQSIQTLSLWLIHHRKHHSTIVKTWIDEVEKADDHRKLTLM 60
           M+ FT++ L+ KL +LN SQQSIQTLSLWLIHHRKHHS IVKTW+ E+++A   +KLT M
Sbjct: 1   MSSFTETGLVKKLFDLNQSQQSIQTLSLWLIHHRKHHSIIVKTWLKELQRAPAAKKLTFM 60

Query: 61  YLANDVIQNSKKKGPEYGKEFGHVLKQAFVSVGDVHCSEKTRSSLSRILNIWEERGVYDK 120
           YLANDVIQNSKKKGPE+G+EF HVL +AF +V       KT +SL+RIL IW +RGVY++
Sbjct: 61  YLANDVIQNSKKKGPEFGREFEHVLVKAFKNVAQSSPEPKTINSLNRILGIWCDRGVYEE 120

Query: 121 QQIASFRTAFNAALEPQTKRRKLSESNTEVLYDVDGNVPIGYFTFFHIDGKGRRNKYDKK 180
            +I  + TA N                TE +  V+            ++G  ++ K D  
Sbjct: 121 PKIKEYSTALNG---------------TETIPRVE------------VNGSDKKRKGDSS 153

Query: 181 QAFVSVGDVHCSEKTRSSLSRILN-IWEERGVYDKQQIASFRTAFNAALEPQTKRRKLSE 239
            A  S G       T S+  +  + + E  G  +     S         EP        E
Sbjct: 154 SAAESEGAKKPRPATVSAEKKAKSEVVEVNGKVETHITLSPHQPDGDPPEP--------E 205

Query: 240 SNTEVLYDVDELETSASSDANIREKIAKLPPEVSEIQLLSKVQGKNITGQPDRVAAENLS 299
              +V+ D   LE SASSDA +RE+IA L PEVSE+  L K++        D+ AA  L+
Sbjct: 206 DLIKVILD---LENSASSDAVVRERIASLKPEVSELAALDKLE--------DKEAAMKLA 254

Query: 300 IQVNEAVDLLTNYNTRLVTEMEDRKRASAMLKDYI 334
             VN+A+ +L +YN RL  EM+DRK+ + ML+D++
Sbjct: 255 ADVNDAIKILNDYNARLAVEMDDRKKLTTMLRDFL 289

Source: Anopheles gambiae str. PEST

Species: Anopheles gambiae

Genus: Anopheles

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	366
FB|FBgn0035318	375	CG9018 [Drosophila melanogaste	0.349	0.341	0.640	9.9e-60
UNIPROTKB|Q5F4B4	325	CREPT "Cell-cycle related and	0.439	0.495	0.478	1.8e-50
UNIPROTKB|A6QLW3	326	RPRD1B "RPRD1B protein" [Bos t	0.439	0.493	0.457	2e-49
UNIPROTKB|E2RRZ8	326	RPRD1B "Uncharacterized protei	0.439	0.493	0.457	2e-49
UNIPROTKB|Q9NQG5	326	RPRD1B "Regulation of nuclear	0.439	0.493	0.457	2e-49
UNIPROTKB|F2Z5H3	326	RPRD1B "Uncharacterized protei	0.439	0.493	0.457	2e-49
MGI|MGI:1917720	326	Rprd1b "regulation of nuclear	0.439	0.493	0.457	2e-49
RGD|1304782	224	Rprd1b "regulation of nuclear	0.439	0.718	0.457	2.8e-42
UNIPROTKB|Q0P5J9	312	RPRD1A "Regulation of nuclear	0.377	0.442	0.496	4.7e-32
UNIPROTKB|Q96P16	312	RPRD1A "Regulation of nuclear	0.377	0.442	0.496	4.7e-32

FB|FBgn0035318 CG9018 [Drosophila melanogaster (taxid:7227)]

 Score = 419 (152.6 bits), Expect = 9.9e-60, Sum P(2) = 9.9e-60
 Identities = 82/128 (64%), Positives = 98/128 (76%)

Query:     1 MAGFTQSALISKLEELNASQQSIQTLSLWLIHHRKHHSTIVKTWIDEVEKADDHRKLTLM 60
             M+ FT SAL+ KL ELN+SQQSIQTLSLWLIHHRKH + IV+TW  E+E   + +KLT M
Sbjct:     1 MSAFTDSALLKKLAELNSSQQSIQTLSLWLIHHRKHSAAIVRTWQRELENVPEPKKLTFM 60

Query:    61 YLANDVIQNSKKKGPEYGKEFGHVLKQAFVSVGDVHCSEKTRSSLSRILNIWEERGVYDK 120
             YLANDVIQNSKKKGPEYGKE+  VL + F  +G+   S+K   SL RILNIW ERGVYD 
Sbjct:    61 YLANDVIQNSKKKGPEYGKEYSLVLGKVFAHIGEKCNSDKLLGSLGRILNIWLERGVYDP 120

Query:   121 QQIASFRT 128
             + IA +R+
Sbjct:   121 KTIADWRS 128

GO:0005575 "cellular_component" evidence=ND

GO:0008150 "biological_process" evidence=ND

GO:0003674 "molecular_function" evidence=ND

UNIPROTKB|Q5F4B4 CREPT "Cell-cycle related and expression-elevated protein in tumor" [Gallus gallus (taxid:9031)]

 Score = 371 (135.7 bits), Expect = 1.8e-50, Sum P(2) = 1.8e-50
 Identities = 79/165 (47%), Positives = 101/165 (61%)

Query:     1 MAGFTQSALISKLEELNASQQSIQTLSLWLIHHRKHHSTIVKTWIDEVEKADDHRKLTLM 60
             M+ F++SAL  KL EL+ SQQS+QTLSLWLIHHRKH   IV  W  E+ KA   RKLT +
Sbjct:     1 MSSFSESALEKKLSELSNSQQSVQTLSLWLIHHRKHAGPIVSVWHRELRKAKSSRKLTFL 60

Query:    61 YLANDVIQNSKKKGPEYGKEFGHVLKQAFVSVGDVHCSEKTRSSLSRILNIWEERGVYDK 120
             YLANDVIQNSK+KGPE+ +EF  VL  AF  V      E  +  L R+LNIW+ER VY  
Sbjct:    61 YLANDVIQNSKRKGPEFTREFESVLVDAFSHVAR-EADEGCKKPLERLLNIWQERSVYGS 119

Query:   121 QQIASFRTAFNAALEPQTKRRK---LSESNTEVLYDVDGNVPIGY 162
             + I   + +   +  PQTK  K   L  +  ++  + D + P  Y
Sbjct:   120 EFIQQLKLSMEDSNSPQTKEEKKSSLKRTFQQIQEEEDDDYPGSY 164

GO:0000993 "RNA polymerase II core binding" evidence=IEA

GO:0008284 "positive regulation of cell proliferation" evidence=IEA

GO:0010564 "regulation of cell cycle process" evidence=IEA

GO:0016591 "DNA-directed RNA polymerase II, holoenzyme" evidence=IEA

GO:0045944 "positive regulation of transcription from RNA polymerase II promoter" evidence=IEA

GO:0070940 "dephosphorylation of RNA polymerase II C-terminal domain" evidence=IEA

UNIPROTKB|A6QLW3 RPRD1B "RPRD1B protein" [Bos taurus (taxid:9913)]

 Score = 357 (130.7 bits), Expect = 2.0e-49, Sum P(2) = 2.0e-49
 Identities = 76/166 (45%), Positives = 101/166 (60%)

Query:     1 MAGFTQSALISKLEELNASQQSIQTLSLWLIHHRKHHSTIVKTWIDEVEKADDHRKLTLM 60
             M+ F++SAL  KL EL+ SQQS+QTLSLWLIHHRKH   IV  W  E+ KA  +RKLT +
Sbjct:     1 MSSFSESALEKKLSELSNSQQSVQTLSLWLIHHRKHAGPIVSVWHRELRKAKSNRKLTFL 60

Query:    61 YLANDVIQNSKKKGPEYGKEFGHVLKQAFVSVGDVHCSEKTRSSLSRILNIWEERGVYDK 120
             YLANDVIQNSK+KGPE+ +EF  VL  AF  V      E  +  L R+LNIW+ER VY  
Sbjct:    61 YLANDVIQNSKRKGPEFTREFESVLVDAFSHVAR-EADEGCKKPLERLLNIWQERSVYGG 119

Query:   121 QQIASFRTAFNAALEPQTK----RRKLSESNTEVLYDVDGNVPIGY 162
             + I   + +   +  P  K    ++ L  +  ++  + D + P  Y
Sbjct:   120 EFIQQLKLSMEDSKSPPPKATEEKKSLKRTFQQIQEEEDDDYPGSY 165

GO:0070940 "dephosphorylation of RNA polymerase II C-terminal domain" evidence=IEA

GO:0045944 "positive regulation of transcription from RNA polymerase II promoter" evidence=IEA

GO:0016591 "DNA-directed RNA polymerase II, holoenzyme" evidence=IEA

GO:0010564 "regulation of cell cycle process" evidence=IEA

GO:0008284 "positive regulation of cell proliferation" evidence=IEA

GO:0000993 "RNA polymerase II core binding" evidence=IEA

UNIPROTKB|E2RRZ8 RPRD1B "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 357 (130.7 bits), Expect = 2.0e-49, Sum P(2) = 2.0e-49
 Identities = 76/166 (45%), Positives = 101/166 (60%)

Query:     1 MAGFTQSALISKLEELNASQQSIQTLSLWLIHHRKHHSTIVKTWIDEVEKADDHRKLTLM 60
             M+ F++SAL  KL EL+ SQQS+QTLSLWLIHHRKH   IV  W  E+ KA  +RKLT +
Sbjct:     1 MSSFSESALEKKLSELSNSQQSVQTLSLWLIHHRKHAGPIVSVWHRELRKAKSNRKLTFL 60

Query:    61 YLANDVIQNSKKKGPEYGKEFGHVLKQAFVSVGDVHCSEKTRSSLSRILNIWEERGVYDK 120
             YLANDVIQNSK+KGPE+ +EF  VL  AF  V      E  +  L R+LNIW+ER VY  
Sbjct:    61 YLANDVIQNSKRKGPEFTREFESVLVDAFSHVAR-EADEGCKKPLERLLNIWQERSVYGG 119

Query:   121 QQIASFRTAFNAALEPQTK----RRKLSESNTEVLYDVDGNVPIGY 162
             + I   + +   +  P  K    ++ L  +  ++  + D + P  Y
Sbjct:   120 EFIQQLKLSMEDSKSPPPKATEEKKSLKRTFQQIQEEEDDDYPGSY 165

GO:0070940 "dephosphorylation of RNA polymerase II C-terminal domain" evidence=IEA

GO:0045944 "positive regulation of transcription from RNA polymerase II promoter" evidence=IEA

GO:0016591 "DNA-directed RNA polymerase II, holoenzyme" evidence=IEA

GO:0010564 "regulation of cell cycle process" evidence=IEA

GO:0008284 "positive regulation of cell proliferation" evidence=IEA

GO:0000993 "RNA polymerase II core binding" evidence=IEA

UNIPROTKB|Q9NQG5 RPRD1B "Regulation of nuclear pre-mRNA domain-containing protein 1B" [Homo sapiens (taxid:9606)]

 Score = 357 (130.7 bits), Expect = 2.0e-49, Sum P(2) = 2.0e-49
 Identities = 76/166 (45%), Positives = 101/166 (60%)

Query:     1 MAGFTQSALISKLEELNASQQSIQTLSLWLIHHRKHHSTIVKTWIDEVEKADDHRKLTLM 60
             M+ F++SAL  KL EL+ SQQS+QTLSLWLIHHRKH   IV  W  E+ KA  +RKLT +
Sbjct:     1 MSSFSESALEKKLSELSNSQQSVQTLSLWLIHHRKHAGPIVSVWHRELRKAKSNRKLTFL 60

Query:    61 YLANDVIQNSKKKGPEYGKEFGHVLKQAFVSVGDVHCSEKTRSSLSRILNIWEERGVYDK 120
             YLANDVIQNSK+KGPE+ +EF  VL  AF  V      E  +  L R+LNIW+ER VY  
Sbjct:    61 YLANDVIQNSKRKGPEFTREFESVLVDAFSHVAR-EADEGCKKPLERLLNIWQERSVYGG 119

Query:   121 QQIASFRTAFNAALEPQTK----RRKLSESNTEVLYDVDGNVPIGY 162
             + I   + +   +  P  K    ++ L  +  ++  + D + P  Y
Sbjct:   120 EFIQQLKLSMEDSKSPPPKATEEKKSLKRTFQQIQEEEDDDYPGSY 165

GO:0006351 "transcription, DNA-dependent" evidence=IEA

GO:0016591 "DNA-directed RNA polymerase II, holoenzyme" evidence=IDA

GO:0070940 "dephosphorylation of RNA polymerase II C-terminal domain" evidence=IMP

GO:0005634 "nucleus" evidence=IDA

GO:0008284 "positive regulation of cell proliferation" evidence=IDA

GO:0010564 "regulation of cell cycle process" evidence=IDA

GO:0045944 "positive regulation of transcription from RNA polymerase II promoter" evidence=IDA

GO:0000993 "RNA polymerase II core binding" evidence=IDA

GO:0005515 "protein binding" evidence=IPI

UNIPROTKB|F2Z5H3 RPRD1B "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 357 (130.7 bits), Expect = 2.0e-49, Sum P(2) = 2.0e-49
 Identities = 76/166 (45%), Positives = 101/166 (60%)

Query:     1 MAGFTQSALISKLEELNASQQSIQTLSLWLIHHRKHHSTIVKTWIDEVEKADDHRKLTLM 60
             M+ F++SAL  KL EL+ SQQS+QTLSLWLIHHRKH   IV  W  E+ KA  +RKLT +
Sbjct:     1 MSSFSESALEKKLSELSNSQQSVQTLSLWLIHHRKHAGPIVSVWHRELRKAKSNRKLTFL 60

Query:    61 YLANDVIQNSKKKGPEYGKEFGHVLKQAFVSVGDVHCSEKTRSSLSRILNIWEERGVYDK 120
             YLANDVIQNSK+KGPE+ +EF  VL  AF  V      E  +  L R+LNIW+ER VY  
Sbjct:    61 YLANDVIQNSKRKGPEFTREFESVLVDAFSHVAR-EADEGCKKPLERLLNIWQERSVYGG 119

Query:   121 QQIASFRTAFNAALEPQTK----RRKLSESNTEVLYDVDGNVPIGY 162
             + I   + +   +  P  K    ++ L  +  ++  + D + P  Y
Sbjct:   120 EFIQQLKLSMEDSKSPPPKATEEKKSLKRTFQQIQEEEDDDYPGSY 165

GO:0070940 "dephosphorylation of RNA polymerase II C-terminal domain" evidence=IEA

GO:0045944 "positive regulation of transcription from RNA polymerase II promoter" evidence=IEA

GO:0016591 "DNA-directed RNA polymerase II, holoenzyme" evidence=IEA

GO:0010564 "regulation of cell cycle process" evidence=IEA

GO:0008284 "positive regulation of cell proliferation" evidence=IEA

GO:0000993 "RNA polymerase II core binding" evidence=IEA

MGI|MGI:1917720 Rprd1b "regulation of nuclear pre-mRNA domain containing 1B" [Mus musculus (taxid:10090)]

 Score = 357 (130.7 bits), Expect = 2.0e-49, Sum P(2) = 2.0e-49
 Identities = 76/166 (45%), Positives = 101/166 (60%)

Query:     1 MAGFTQSALISKLEELNASQQSIQTLSLWLIHHRKHHSTIVKTWIDEVEKADDHRKLTLM 60
             M+ F++SAL  KL EL+ SQQS+QTLSLWLIHHRKH   IV  W  E+ KA  +RKLT +
Sbjct:     1 MSSFSESALEKKLSELSNSQQSVQTLSLWLIHHRKHAGPIVSVWHRELRKAKSNRKLTFL 60

Query:    61 YLANDVIQNSKKKGPEYGKEFGHVLKQAFVSVGDVHCSEKTRSSLSRILNIWEERGVYDK 120
             YLANDVIQNSK+KGPE+ +EF  VL  AF  V      E  +  L R+LNIW+ER VY  
Sbjct:    61 YLANDVIQNSKRKGPEFTREFESVLVDAFSHVAR-EADEGCKKPLERLLNIWQERSVYGG 119

Query:   121 QQIASFRTAFNAALEPQTK----RRKLSESNTEVLYDVDGNVPIGY 162
             + I   + +   +  P  K    ++ L  +  ++  + D + P  Y
Sbjct:   120 EFIQQLKLSMEDSKSPPPKAAEEKKSLKRTFQQIQEEEDDDYPGSY 165

GO:0000993 "RNA polymerase II core binding" evidence=ISO

GO:0005634 "nucleus" evidence=ISO

GO:0006351 "transcription, DNA-dependent" evidence=IEA

GO:0006355 "regulation of transcription, DNA-dependent" evidence=IEA

GO:0008284 "positive regulation of cell proliferation" evidence=ISO

GO:0010564 "regulation of cell cycle process" evidence=ISO

GO:0016591 "DNA-directed RNA polymerase II, holoenzyme" evidence=ISO

GO:0045944 "positive regulation of transcription from RNA polymerase II promoter" evidence=ISO

GO:0070940 "dephosphorylation of RNA polymerase II C-terminal domain" evidence=ISO

RGD|1304782 Rprd1b "regulation of nuclear pre-mRNA domain containing 1B" [Rattus norvegicus (taxid:10116)]

 Score = 357 (130.7 bits), Expect = 2.8e-42, Sum P(2) = 2.8e-42
 Identities = 76/166 (45%), Positives = 101/166 (60%)

Query:     1 MAGFTQSALISKLEELNASQQSIQTLSLWLIHHRKHHSTIVKTWIDEVEKADDHRKLTLM 60
             M+ F++SAL  KL EL+ SQQS+QTLSLWLIHHRKH   IV  W  E+ KA  +RKLT +
Sbjct:     1 MSSFSESALEKKLSELSNSQQSVQTLSLWLIHHRKHAGPIVSVWHRELRKAKSNRKLTFL 60

Query:    61 YLANDVIQNSKKKGPEYGKEFGHVLKQAFVSVGDVHCSEKTRSSLSRILNIWEERGVYDK 120
             YLANDVIQNSK+KGPE+ +EF  VL  AF  V      E  +  L R+LNIW+ER VY  
Sbjct:    61 YLANDVIQNSKRKGPEFTREFESVLVDAFSHVAR-EADEGCKKPLERLLNIWQERSVYGG 119

Query:   121 QQIASFRTAFNAALEPQTK----RRKLSESNTEVLYDVDGNVPIGY 162
             + I   + +   +  P  K    ++ L  +  ++  + D + P  Y
Sbjct:   120 EFIQQLKLSMEDSKSPPPKAAEEKKSLKRTFQQIQEEEDDDYPGSY 165

GO:0000993 "RNA polymerase II core binding" evidence=ISO

GO:0005634 "nucleus" evidence=ISO

GO:0008284 "positive regulation of cell proliferation" evidence=ISO

GO:0010564 "regulation of cell cycle process" evidence=ISO

GO:0016591 "DNA-directed RNA polymerase II, holoenzyme" evidence=ISO

GO:0045944 "positive regulation of transcription from RNA polymerase II promoter" evidence=ISO

GO:0070940 "dephosphorylation of RNA polymerase II C-terminal domain" evidence=ISO

UNIPROTKB|Q0P5J9 RPRD1A "Regulation of nuclear pre-mRNA domain-containing protein 1A" [Bos taurus (taxid:9913)]

 Score = 351 (128.6 bits), Expect = 4.7e-32, P = 4.7e-32
 Identities = 69/139 (49%), Positives = 92/139 (66%)

Query:     1 MAGFTQSALISKLEELNASQQSIQTLSLWLIHHRKHHSTIVKTWIDEVEKADDHRKLTLM 60
             M+ F+++AL  KL EL+ SQQS+QTLSLWLIHHRKH   IV  W  E+ KA  +RKLT +
Sbjct:     1 MSAFSEAALEKKLSELSNSQQSVQTLSLWLIHHRKHSRPIVTVWERELRKAKPNRKLTFL 60

Query:    61 YLANDVIQNSKKKGPEYGKEFGHVLKQAFVSVGDVHCSEKTRSSLSRILNIWEERGVYDK 120
             YLANDVIQNSK+KGPE+ K+F  V+ +AF  V      E  +  L R+L+IWEER VY+ 
Sbjct:    61 YLANDVIQNSKRKGPEFTKDFAPVIVEAFKHVSS-ETDESCKKHLGRVLSIWEERSVYEN 119

Query:   121 QQIASFRTAFNAALEPQTK 139
               +   + A     +P+ +
Sbjct:   120 DVLEQLKQALYGDKKPRKR 138

GO:0016591 "DNA-directed RNA polymerase II, holoenzyme" evidence=ISS

GO:0070940 "dephosphorylation of RNA polymerase II C-terminal domain" evidence=ISS

UNIPROTKB|Q96P16 RPRD1A "Regulation of nuclear pre-mRNA domain-containing protein 1A" [Homo sapiens (taxid:9606)]

 Score = 351 (128.6 bits), Expect = 4.7e-32, P = 4.7e-32
 Identities = 69/139 (49%), Positives = 92/139 (66%)

Query:     1 MAGFTQSALISKLEELNASQQSIQTLSLWLIHHRKHHSTIVKTWIDEVEKADDHRKLTLM 60
             M+ F+++AL  KL EL+ SQQS+QTLSLWLIHHRKH   IV  W  E+ KA  +RKLT +
Sbjct:     1 MSAFSEAALEKKLSELSNSQQSVQTLSLWLIHHRKHSRPIVTVWERELRKAKPNRKLTFL 60

Query:    61 YLANDVIQNSKKKGPEYGKEFGHVLKQAFVSVGDVHCSEKTRSSLSRILNIWEERGVYDK 120
             YLANDVIQNSK+KGPE+ K+F  V+ +AF  V      E  +  L R+L+IWEER VY+ 
Sbjct:    61 YLANDVIQNSKRKGPEFTKDFAPVIVEAFKHVSS-ETDESCKKHLGRVLSIWEERSVYEN 119

Query:   121 QQIASFRTAFNAALEPQTK 139
               +   + A     +P+ +
Sbjct:   120 DVLEQLKQALYGDKKPRKR 138

GO:0016591 "DNA-directed RNA polymerase II, holoenzyme" evidence=IDA

GO:0070940 "dephosphorylation of RNA polymerase II C-terminal domain" evidence=IMP

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

No confident hit for EC number transfering in SWISSPROT detected by BLAST

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	366
smart00582	124	smart00582, RPR, domain present in proteins, which	1e-34
cd03562	114	cd03562, CID, CID (CTD-Interacting Domain) domain	5e-33
pfam04818	64	pfam04818, CTD_bind, RNA polymerase II-binding dom	1e-16
pfam12243	139	pfam12243, CTK3, CTD kinase subunit gamma CTK3	7e-05
smart00582	124	smart00582, RPR, domain present in proteins, which	0.001
cd03562	114	cd03562, CID, CID (CTD-Interacting Domain) domain	0.001

>gnl|CDD|214731 smart00582, RPR, domain present in proteins, which are involved in regulation of nuclear pre-mRNA

 Score =  123 bits (310), Expect = 1e-34
 Identities = 53/125 (42%), Positives = 72/125 (57%), Gaps = 2/125 (1%)

Query: 8   ALISKLEELNASQQSIQTLSLWLIHHRKHHSTIVKTWIDEVEKADDHRKLTLMYLANDVI 67
           A   KLE LN SQ+SIQTL+ W I H  H   IV+ W   ++KA   RKL L+YL + ++
Sbjct: 1   AFEQKLESLNNSQESIQTLTKWAIEHASHAKEIVELWEKYIKKAPVPRKLPLLYLLDSIV 60

Query: 68  QNSK-KKGPEYGKEFGHVLKQAFVSVGDVHCSEKTRSSLSRILNIWEERGVYDKQQIASF 126
           QNSK K G E+G E G V + A   V      E+ +  + R+LNIWEERG++  + +   
Sbjct: 61  QNSKRKYGSEFGDELGPVFQDALRRVLG-AAPEELKKKIRRLLNIWEERGIFPPEVLRPL 119

Query: 127 RTAFN 131
           R   N
Sbjct: 120 REKLN 124

Length = 124

>gnl|CDD|239621 cd03562, CID, CID (CTD-Interacting Domain) domain family; CID is present in several RNA-processing factors such as Pcf11 and Nrd1

 Score =  118 bits (299), Expect = 5e-33
 Identities = 43/122 (35%), Positives = 62/122 (50%), Gaps = 14/122 (11%)

Query: 4   FTQSALISKLEELNASQQSIQTLSLWLIHHRKHHSTIVKTWIDEVEKADDHRKLTLMYLA 63
           F  +AL+ KL     SQ SIQTL+   I +RKH   IV+     ++K    +KL L+YL 
Sbjct: 2   FDYNALLEKLTFNKNSQPSIQTLTKLAIENRKHAKEIVEIIEKHIKKCPPEQKLPLLYLL 61

Query: 64  NDVIQNSKKKGPEYGKE-----FGHVLKQAFVSVGDVHCSEKTRSSLSRILNIWEERGVY 118
           + +++N  +K  E+  E     F    ++           EKTR  L R+LNIWEER V+
Sbjct: 62  DSIVKNVGRKYKEFFSEFLVPLFLDAYEK---------VDEKTRKKLERLLNIWEERFVF 112

Query: 119 DK 120
             
Sbjct: 113 GS 114

Pcf11 is a conserved and essential subunit of the yeast cleavage factor IA, which is required for polyadenylation-dependent 3'-RNA processing and transcription termination. Nrd1 is implicated in polyadenylation-independent 3'-RNA processing. CID binds tightly to the carboxy-terminal domain (CTD) of RNA polymerase (Pol) II. During transcription, Pol II synthesizes eukaryotic messenger RNA. Transcription is coupled to RNA processing through the CTD, which consists of up to 52 repeats of the sequence Tyr 1-Ser 2-Pro 3-Thr 4-Ser 5-Pro 6-Ser 7. CID contains eight alpha-helices in a right-handed superhelical arrangement, which closely resembles that of the VHS domains and ARM (Armadillo) repeat proteins, except for its two amino-terminal helices. Length = 114

>gnl|CDD|218279 pfam04818, CTD_bind, RNA polymerase II-binding domain

 Score = 73.0 bits (180), Expect = 1e-16
 Identities = 32/65 (49%), Positives = 40/65 (61%), Gaps = 2/65 (3%)

Query: 56  KLTLMYLANDVIQNSKKKGP-EYGKEFGHVLKQAFVSVGDVHCSEKTRSSLSRILNIWEE 114
           KL L+YLANDV+QNSK K   E+ K F  VL  AF  V      E+ +  + R+LNIWEE
Sbjct: 1   KLPLLYLANDVVQNSKHKNKDEFVKAFSPVLPDAFAHVY-KEGDEEVKKKIRRLLNIWEE 59

Query: 115 RGVYD 119
           R V+ 
Sbjct: 60  RNVFS 64

This domain binds to the phosphorylated C-terminal domain (CTD) of RNA polymerase II. Length = 64

>gnl|CDD|192965 pfam12243, CTK3, CTD kinase subunit gamma CTK3

 Score = 42.0 bits (99), Expect = 7e-05
 Identities = 21/125 (16%), Positives = 52/125 (41%), Gaps = 6/125 (4%)

Query: 5   TQSALISKLEELNASQQSIQTLSLWLIHHRKHHSTIVKTWIDEVEKADDHRKLTLMYLAN 64
            +S     L  LNAS QS+Q  + + + +      +    ++++E    + +  +MY  +
Sbjct: 6   VRSRFTQLLRHLNASVQSLQKAASFALKYSDMEEDLHSCILEQLEDGSLNTRANIMYFID 65

Query: 65  DVIQNSKKKGPEYGKEFGHVLKQAFVSVGDVHCSEKTRSSLS-----RILNIWEERGVYD 119
            + + + K+G      +  +L++    + D    E+   + +     ++L    +R V D
Sbjct: 66  TLCEMALKEGK-SHNPYVRMLQRDIPRLVDSVVPEENSGAANLKSVRKVLQTLRKRLVLD 124

Query: 120 KQQIA 124
            +   
Sbjct: 125 PETYE 129

The C-terminal domain kinase (CTDK-1), is a three-subunit complex comprised of Ctk1, Ctk2, and Ctk3, that plays a key role in regulation of transcription and translation and in coordinating these two processes. Both Ctk2 and Ctk3 are regulated at the level of protein turnover, and are unstable proteins processed through a ubiquitin-proteasome pathway. Their physical interaction is required to protect both subunits from degradation, and both Ctk2 and Ctk3 are required for Ctk1 CTD kinase activation. The mammalian P-TEFb is mirrored by the combined complexes in yeast of the CTDK1 and the Bur1/2. Length = 139

>gnl|CDD|214731 smart00582, RPR, domain present in proteins, which are involved in regulation of nuclear pre-mRNA

 Score = 38.0 bits (89), Expect = 0.001
 Identities = 12/36 (33%), Positives = 20/36 (55%)

Query: 190 HCSEKTRSSLSRILNIWEERGVYDKQQIASFRTAFN 225
              E+ +  + R+LNIWEERG++  + +   R   N
Sbjct: 89  AAPEELKKKIRRLLNIWEERGIFPPEVLRPLREKLN 124

Length = 124

>gnl|CDD|239621 cd03562, CID, CID (CTD-Interacting Domain) domain family; CID is present in several RNA-processing factors such as Pcf11 and Nrd1

 Score = 38.0 bits (89), Expect = 0.001
 Identities = 19/46 (41%), Positives = 24/46 (52%), Gaps = 3/46 (6%)

Query: 172 GRRNKYDKKQAFVSV-GDV--HCSEKTRSSLSRILNIWEERGVYDK 214
           GR+ K    +  V +  D      EKTR  L R+LNIWEER V+  
Sbjct: 69  GRKYKEFFSEFLVPLFLDAYEKVDEKTRKKLERLLNIWEERFVFGS 114

Pcf11 is a conserved and essential subunit of the yeast cleavage factor IA, which is required for polyadenylation-dependent 3'-RNA processing and transcription termination. Nrd1 is implicated in polyadenylation-independent 3'-RNA processing. CID binds tightly to the carboxy-terminal domain (CTD) of RNA polymerase (Pol) II. During transcription, Pol II synthesizes eukaryotic messenger RNA. Transcription is coupled to RNA processing through the CTD, which consists of up to 52 repeats of the sequence Tyr 1-Ser 2-Pro 3-Thr 4-Ser 5-Pro 6-Ser 7. CID contains eight alpha-helices in a right-handed superhelical arrangement, which closely resembles that of the VHS domains and ARM (Armadillo) repeat proteins, except for its two amino-terminal helices. Length = 114

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	366
KOG2669|consensus	325		100.0
smart00582	121	RPR domain present in proteins, which are involved	99.95
cd03562	114	CID CID (CTD-Interacting Domain) domain family; CI	99.91
PF04818	64	CTD_bind: RNA polymerase II-binding domain.; Inter	99.75
KOG0151|consensus	877		99.67
PF12243	139	CTK3: CTD kinase subunit gamma CTK3	99.59
KOG4368|consensus	757		99.12
KOG2669|consensus	325		98.75
KOG0132|consensus	894		98.56
KOG2071|consensus	579		97.63
PF04818	64	CTD_bind: RNA polymerase II-binding domain.; Inter	92.53
cd00197	115	VHS_ENTH_ANTH VHS, ENTH and ANTH domain superfamil	92.19
PF00790	140	VHS: VHS domain; InterPro: IPR002014 The VHS domai	91.85
cd03561	133	VHS VHS domain family; The VHS domain is present i	89.76
smart00582	121	RPR domain present in proteins, which are involved	86.81
smart00288	133	VHS Domain present in VPS-27, Hrs and STAM. Unpubl	86.25
cd03567	139	VHS_GGA VHS domain family, GGA subfamily; GGA (Gol	81.92

>KOG2669|consensus

Probab=100.00  E-value=1.7e-50  Score=391.89  Aligned_cols=284  Identities=37%  Similarity=0.561  Sum_probs=236.5

Q ss_pred             CCCCCHHHHHHHHHhccccHHHHHHHHHHHhhhccchhHHHHHHHHHHhhcCcccchhHHHHhHHHHHHhhhcCcchHHH
Q psy15160          1 MAGFTQSALISKLEELNASQQSIQTLSLWLIHHRKHHSTIVKTWIDEVEKADDHRKLTLMYLANDVIQNSKKKGPEYGKE   80 (366)
Q Consensus         1 M~~Fse~~l~~kL~~L~~Sq~SIqtlS~W~l~h~k~a~~IV~~w~~~L~ka~~~kKL~lLYLaNDVlQnskkkg~~f~~~   80 (366)
                      ||+||+++|.++|++|++||+||||+|.|||+|++||+.||++|+++|+++..++||+||||||||||||+|+|++|+++
T Consensus         1 m~~fsee~l~~kL~~L~~TQeSIqtlS~Wli~hkk~a~~IV~~Wl~~~~~~~~~~Kl~llYLaNDVvQnskrk~~ef~~e   80 (325)
T KOG2669|consen    1 MSAFSEEALEKKLAELSNTQESIQTLSLWLIHHKKHARLIVDVWLKELKKSSVNHKLTLLYLANDVVQNSKRKGPEFVDE   80 (325)
T ss_pred             CCcccHHHHHHHHHhccchHHHHHHHHHHHHHHhhhhhHHHHHHHHHHhccCCCceeeehhhhHHHHHHhhhcCchhHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHhcccCCChHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHhhcCcccccccccccccccccccCCCCCC
Q psy15160         81 FGHVLKQAFVSVGDVHCSEKTRSSLSRILNIWEERGVYDKQQIASFRTAFNAALEPQTKRRKLSESNTEVLYDVDGNVPI  160 (366)
Q Consensus        81 F~~vL~~af~~i~~~~~d~~~~~kv~RIL~IW~eR~Vy~~~~i~~L~~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  160 (366)
                      |+++++.+|.+++ ...+.+++++|.||++||++|+||+++++..|+..|+ .  +.  |++...               
T Consensus        81 f~~v~~~a~~~i~-~~~~~~~k~~l~Rl~nIw~eR~Vf~~~~~~~l~~~l~-~--e~--p~~~d~---------------  139 (325)
T KOG2669|consen   81 FWPVVLKAFAHIV-EETDVKCKKKLGRLINIWEERNVFSPESLVDLEESLG-A--EK--PPPLDE---------------  139 (325)
T ss_pred             HHHHHHHHHHHHH-HhcchhhhHHHHHHHHHHHHhccCCHHHHHHHHHHhc-c--cC--Ccchhh---------------
Confidence            9999999999999 5777888999999999999999999999999999997 1  11  110001               


Q ss_pred             CccccccccCCCccccccccccccccccccCCccccccccchhchhhccccchhhHHHHHHHhhhhccCcchhhcCCCcc
Q psy15160        161 GYFTFFHIDGKGRRNKYDKKQAFVSVGDVHCSEKTRSSLSRILNIWEERGVYDKQQIASFRTAFNAALEPQTKRRKLSES  240 (366)
Q Consensus       161 ~~~~~~~~~~~~~k~~~~~~~af~hva~~~~dek~~~~l~r~l~Iw~er~vye~~~i~~~~~~~~~~~~~~~~~~k~p~~  240 (366)
                               .+.+++..+.+.                        -.+++.+..+.+           ....  ..+...
T Consensus       140 ---------~~~~~~~~~~~k------------------------~~~~~~~~~~~~-----------~~~v--~~~~~~  173 (325)
T KOG2669|consen  140 ---------AKKLPRGSKQIK------------------------LDEKGSKPGLSS-----------LGEV--HEKIDS  173 (325)
T ss_pred             ---------hhccccchHhhh------------------------hhhhccCCCCCC-----------cccc--chhHHh
Confidence                     111111111111                        001111100000           0000  001112


Q ss_pred             hhhHhhhhhhhhcccC-CcHHHHHHhhcCCCCchhhhhhHhhhCCCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy15160        241 NTEVLYDVDELETSAS-SDANIREKIAKLPPEVSEIQLLSKVQGKNITGQPDRVAAENLSIQVNEAVDLLTNYNTRLVTE  319 (366)
Q Consensus       241 ~~eli~~l~~~e~s~s-Sp~~~r~~ia~lpPEveel~~L~~Led~~~~~~~~~~~~~~l~~~v~ea~~~l~~y~~rL~~e  319 (366)
                      ..+++.+.+++++.++ +++.++++|+.+|.+++|.+.+.++.++        ..++.+++.+++++++|.+|+.||+++
T Consensus       174 ~~~l~~a~~s~~~~~~k~~~~~~~~i~~~~~e~~e~~~~~k~~~~--------~~~e~~~k~lee~~~lL~e~~~~L~s~  245 (325)
T KOG2669|consen  174 SVELVRALQSLENAASKLDAVLEERIARLPQEVEEVSSLEKITLN--------SLIESLAKHLEEEEMLLREVNPRLAAE  245 (325)
T ss_pred             HHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHhhhH--------HHHHHHHHHHHHHHHHHHHHHHHhccc
Confidence            4567788888888888 8999999999999999999999999999        999999999999999999999999999


Q ss_pred             HhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy15160        320 MEDRKRASAMLKDYIAAQRELLEQAEQRLEVSETEIFLFL  359 (366)
Q Consensus       320 ~~~r~~l~~~L~~~~~~q~~~~~~~~~~l~e~~~~~~~~~  359 (366)
                      +.+|.++..||++++..|.+.+...+..+++++.+++...
T Consensus       246 ~~~~~~~~~~l~d~l~~q~~~l~~~~~~~~~~k~~l~~~~  285 (325)
T KOG2669|consen  246 EESRRQLVSMLRDALREQKEELNDEEPQLEEYKEKLDKAQ  285 (325)
T ss_pred             chhhhhhHHHHHHHHhhhhccccccccCchhhhhhHHHHh
Confidence            9999999999999999999999999999999999998654

>smart00582 RPR domain present in proteins, which are involved in regulation of nuclear pre-mRNA

Probab=99.95  E-value=1.3e-27  Score=202.44  Aligned_cols=119  Identities=44%  Similarity=0.765  Sum_probs=113.1

Q ss_pred             HHHHHHHhccccHHHHHHHHHHHhhhccchhHHHHHHHHHHhhcCcccchhHHHHhHHHHHHhhhc-CcchHHHHHHHHH
Q psy15160          8 ALISKLEELNASQQSIQTLSLWLIHHRKHHSTIVKTWIDEVEKADDHRKLTLMYLANDVIQNSKKK-GPEYGKEFGHVLK   86 (366)
Q Consensus         8 ~l~~kL~~L~~Sq~SIqtlS~W~l~h~k~a~~IV~~w~~~L~ka~~~kKL~lLYLaNDVlQnskkk-g~~f~~~F~~vL~   86 (366)
                      +|.++|++|++|+++|++++.||++|.+++..||++|.+++.++++++||++|||+|||+|||+++ ++.|...|.++++
T Consensus         1 ~f~~~L~~L~~s~~~I~~lt~~~~~~~~~a~~Iv~~i~~~~~~~~~~~kL~~LYlindIl~n~~~~~~~~f~~~~~~~~~   80 (121)
T smart00582        1 AFEQKLESLNNSQESIQTLTKWAIEHASHAKEIVELWEKYIKKAPPPRKLPLLYLLDSIVQNSKRKYGSEFGDELGPVFQ   80 (121)
T ss_pred             ChHHHHHhccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCccceehhHHhHHHHHHHHhhccHHHHHHHHHHHHH
Confidence            478999999999999999999999999999999999999999999999999999999999999987 6789999999999


Q ss_pred             HHHHHhcccCCChHHHHHHHHHHHHhhhCCCCCHHHHHHHH
Q psy15160         87 QAFVSVGDVHCSEKTRSSLSRILNIWEERGVYDKQQIASFR  127 (366)
Q Consensus        87 ~af~~i~~~~~d~~~~~kv~RIL~IW~eR~Vy~~~~i~~L~  127 (366)
                      .+|.+++. ..+++.++++.+||++|++|+||++++|..|+
T Consensus        81 ~~~~~~~~-~~~~~~~~ki~kll~iW~~~~iF~~~~i~~L~  120 (121)
T smart00582       81 DALRDVLG-AANDETKKKIRRLLNIWEERGIFPPSVLRPLR  120 (121)
T ss_pred             HHHHHHHH-hCCHHHHHHHHHHHHHHhcCCCCCHHHHHHhh
Confidence            99999993 45689999999999999999999999999987

>cd03562 CID CID (CTD-Interacting Domain) domain family; CID is present in several RNA-processing factors such as Pcf11 and Nrd1

Probab=99.91  E-value=3.3e-24  Score=180.35  Aligned_cols=114  Identities=39%  Similarity=0.529  Sum_probs=104.1

Q ss_pred             CCCHHHHHHHHHhccccHHHHHHHHHHHhhhccchhHHHHHHHHHHhhcCcccchhHHHHhHHHHHHhhhcCcchHHHHH
Q psy15160          3 GFTQSALISKLEELNASQQSIQTLSLWLIHHRKHHSTIVKTWIDEVEKADDHRKLTLMYLANDVIQNSKKKGPEYGKEFG   82 (366)
Q Consensus         3 ~Fse~~l~~kL~~L~~Sq~SIqtlS~W~l~h~k~a~~IV~~w~~~L~ka~~~kKL~lLYLaNDVlQnskkkg~~f~~~F~   82 (366)
                      .|+...+.++|..+++|+.+|++++.||++|++++..||++|.++++++++.+||++|||+|||+||+++++..   .|.
T Consensus         1 ~~~~~~~l~~L~~~~~S~~~I~~lt~~a~~~~~~a~~iv~~i~~~i~~~~~~~KL~~LYL~dsIvkn~~~~~~~---~~~   77 (114)
T cd03562           1 VFDYNALLEKLTFNKNSQPSIQTLTKLAIENRKHAKEIVEIIEKHIKKCPPEQKLPLLYLLDSIVKNVGRKYKE---FFS   77 (114)
T ss_pred             CccHHHHHHHHHcCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCcccchHHHHHHHHHHHHcccchHH---HHH
Confidence            36778999999999999999999999999999999999999999999999999999999999999998877543   456


Q ss_pred             HHHHHHHHHhcccCCChHHHHHHHHHHHHhhhCCCCCH
Q psy15160         83 HVLKQAFVSVGDVHCSEKTRSSLSRILNIWEERGVYDK  120 (366)
Q Consensus        83 ~vL~~af~~i~~~~~d~~~~~kv~RIL~IW~eR~Vy~~  120 (366)
                      ..++++|.+++ ...|++++.++.||+++|++|++|+.
T Consensus        78 ~~~~~~f~~~~-~~~~~~~r~kl~rl~~iW~~~~~f~~  114 (114)
T cd03562          78 EFLVPLFLDAY-EKVDEKTRKKLERLLNIWEERFVFGS  114 (114)
T ss_pred             HHHHHHHHHHH-HhCCHHHHHHHHHHHHHccCCCCCCC
Confidence            66688999998 57899999999999999999999973

Pcf11 is a conserved and essential subunit of the yeast cleavage factor IA, which is required for polyadenylation-dependent 3'-RNA processing and transcription termination. Nrd1 is implicated in polyadenylation-independent 3'-RNA processing. CID binds tightly to the carboxy-terminal domain (CTD) of RNA polymerase (Pol) II. During transcription, Pol II synthesizes eukaryotic messenger RNA. Transcription is coupled to RNA processing through the CTD, which consists of up to 52 repeats of the sequence Tyr 1-Ser 2-Pro 3-Thr 4-Ser 5-Pro 6-Ser 7. CID contains eight alpha-helices in a right-handed superhelical arrangement, which closely resembles that of the VHS domains and ARM (Armadillo) repeat proteins, except for its two amino-terminal helices.

>PF04818 CTD_bind: RNA polymerase II-binding domain

Probab=99.75  E-value=1.2e-18  Score=132.82  Aligned_cols=63  Identities=46%  Similarity=0.841  Sum_probs=58.3

Q ss_pred             chhHHHHhHHHHHHhhhcCc-chHHHHHHHHHHHHHHhcccCCChHHHHHHHHHHHHhhhCCCCC
Q psy15160         56 KLTLMYLANDVIQNSKKKGP-EYGKEFGHVLKQAFVSVGDVHCSEKTRSSLSRILNIWEERGVYD  119 (366)
Q Consensus        56 KL~lLYLaNDVlQnskkkg~-~f~~~F~~vL~~af~~i~~~~~d~~~~~kv~RIL~IW~eR~Vy~  119 (366)
                      ||++|||||||+|||+++++ +|..+|+++||.+|.+++ ...+++.+++|.||++||++|+||+
T Consensus         1 KL~~lYl~ndI~q~sk~k~~~~f~~~F~~~l~~~~~~~~-~~~~~~~~~kv~rll~iW~~r~if~   64 (64)
T PF04818_consen    1 KLALLYLANDILQNSKRKNPDEFAPAFSPVLPDAFAHAY-KNVDPEVRKKVQRLLNIWEERNIFS   64 (64)
T ss_dssp             HHHHHHHHHHHHHHHHHHTTHCHHHHHHCCHHHHHHHHC-CCS-HHHHHHHHHHHHHHHHCTSS-
T ss_pred             CcceeehHHHHHHHhhhcChHHHHHHHHHHHHHHHHHHH-hcCCHHHHHHHHHHHHHhhCCCCCC
Confidence            79999999999999999987 999999999999999999 5669999999999999999999996

; InterPro: IPR006903 This entry represents a conserved region found in a number of uncharacterised eukaryotic proteins.; PDB: 2L0I_A 2KM4_A 3D9I_B 3D9N_B 3D9O_A 3D9P_B 3D9K_A 3D9M_A 3D9J_A 3D9L_A ....

>KOG0151|consensus

Probab=99.67  E-value=1.6e-16  Score=165.50  Aligned_cols=132  Identities=17%  Similarity=0.398  Sum_probs=117.7

Q ss_pred             CCCCCHHHHHHHHHhccccHHHHHHHHHHHhhhccchhHHHHHHHHHHh--hcCcccchhHHHHhHHHHHHhhhc--C-c
Q psy15160          1 MAGFTQSALISKLEELNASQQSIQTLSLWLIHHRKHHSTIVKTWIDEVE--KADDHRKLTLMYLANDVIQNSKKK--G-P   75 (366)
Q Consensus         1 M~~Fse~~l~~kL~~L~~Sq~SIqtlS~W~l~h~k~a~~IV~~w~~~L~--ka~~~kKL~lLYLaNDVlQnskkk--g-~   75 (366)
                      |+....+.|+..|+.||.-..||..++.||+.|.+.|.+||+|+.+.|.  .++..+||+.|||+||||+||..+  + .
T Consensus       428 Ltd~qRdklE~liR~LTpEk~sIg~aM~FalenA~aa~EI~eci~eSlt~~~t~~~kKiarLyLvsDIL~N~sarv~nas  507 (877)
T KOG0151|consen  428 LTDLQRDKLEDLIRGLTPEKSSIGDAMVFALENADAAGEIVECITESLTNKETPLPKKIARLYLVSDILHNSSARVANAS  507 (877)
T ss_pred             cchHHHHHHHHHHHhcCcccchHHHHHHHHHhhhhhHHHHHHHHHHHHhccCCcchhHHHHHHHHHHHHhhhhhhhhHHH
Confidence            3445678999999999999999999999999999999999999999986  478899999999999999999866  2 4


Q ss_pred             chHHHHHHHHHHHHHHhcc---c----CCChHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHh
Q psy15160         76 EYGKEFGHVLKQAFVSVGD---V----HCSEKTRSSLSRILNIWEERGVYDKQQIASFRTAFNA  132 (366)
Q Consensus        76 ~f~~~F~~vL~~af~~i~~---~----~~d~~~~~kv~RIL~IW~eR~Vy~~~~i~~L~~~L~~  132 (366)
                      -|+..|++.|+.+|..++.   +    ...+..+++|..||.+|++|-||+.++|..|++.+..
T Consensus       508 ~YR~~FEa~L~~Ifd~l~~~yr~I~gRIkaE~fkqRV~kVirvWedW~ifpe~~l~~l~~~Flg  571 (877)
T KOG0151|consen  508 AYRKSFEATLEDIFDDLNDLYRSIGGRIKAEAFKQRVMKVIRVWEDWAIFPEDFLIGLQNTFLG  571 (877)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhccchhhHHHHHHHHHHHHHHHHHHHhCcHHHHHHHHHHHhc
Confidence            7999999999999998763   1    1346779999999999999999999999999998864

>PF12243 CTK3: CTD kinase subunit gamma CTK3

Probab=99.59  E-value=3e-14  Score=124.88  Aligned_cols=126  Identities=19%  Similarity=0.346  Sum_probs=115.8

Q ss_pred             HHHHHHHHHhccccHHHHHHHHHHHhhhccchhHHHHHHHHHHhhcCcccchhHHHHhHHHHHHhhhcC---cchHHHHH
Q psy15160          6 QSALISKLEELNASQQSIQTLSLWLIHHRKHHSTIVKTWIDEVEKADDHRKLTLMYLANDVIQNSKKKG---PEYGKEFG   82 (366)
Q Consensus         6 e~~l~~kL~~L~~Sq~SIqtlS~W~l~h~k~a~~IV~~w~~~L~ka~~~kKL~lLYLaNDVlQnskkkg---~~f~~~F~   82 (366)
                      .-+|.+.|+.||+|++|||.+..|.|.|+..++.+..|+++.|.+.+.+.|+++||++..+++-|.+.+   ..|+...+
T Consensus         7 r~~F~~~L~~L~aS~qSi~kaa~fAlk~~~~~edL~~cIle~le~~~lN~R~nI~~fID~l~e~~~~~~~~~~~Yv~~l~   86 (139)
T PF12243_consen    7 RMQFTQLLRRLNASQQSIQKAAQFALKNRDMEEDLWSCILEQLEKENLNTRINIFYFIDSLCESSQKSKKYNYPYVSMLQ   86 (139)
T ss_pred             HHHHHHHHHHcchhHHHHHHHHHHHHHccccHHHHHHHHHHHHhccchhhHHHHHHHHHHHHHHHHhcccccchhHHHHH
Confidence            458999999999999999999999999999999999999999999999999999999999999988654   58999999


Q ss_pred             HHHHHHHHHhcccCCC-hHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHH
Q psy15160         83 HVLKQAFVSVGDVHCS-EKTRSSLSRILNIWEERGVYDKQQIASFRTAFN  131 (366)
Q Consensus        83 ~vL~~af~~i~~~~~d-~~~~~kv~RIL~IW~eR~Vy~~~~i~~L~~~L~  131 (366)
                      ..||.++..|++.+.. ....+.+.+||+.|.+|.++++..+.++...|.
T Consensus        87 ~dL~~Iv~~V~P~~~~g~~N~~~~~kvL~~~~~k~~l~~~~~~~~~~~l~  136 (139)
T PF12243_consen   87 RDLPRIVDAVAPPDNSGAANLKSVRKVLKNWSKKKILDPEEYEEIEASLK  136 (139)
T ss_pred             HHHHHHHHHhCCCCCccchHHHHHHHHHHHHHHcCCCCHHHHHHHHHHHh
Confidence            9999999999963322 367999999999999999999999999998885

>KOG4368|consensus

Probab=99.12  E-value=2.6e-10  Score=117.46  Aligned_cols=124  Identities=19%  Similarity=0.404  Sum_probs=101.4

Q ss_pred             HHHHHHHHHhc--cccHHHHHHHHHHHhhhcc---chhHHHHHHHHHHhh--cCcccchhHHHHhHHHHHHhhhcC-cch
Q psy15160          6 QSALISKLEEL--NASQQSIQTLSLWLIHHRK---HHSTIVKTWIDEVEK--ADDHRKLTLMYLANDVIQNSKKKG-PEY   77 (366)
Q Consensus         6 e~~l~~kL~~L--~~Sq~SIqtlS~W~l~h~k---~a~~IV~~w~~~L~k--a~~~kKL~lLYLaNDVlQnskkkg-~~f   77 (366)
                      -..|...|+-+  ++|.+.|.....||..+.+   |++.|+.+....++.  +...-+|++|||+|||+++|.+|. .+.
T Consensus       103 ~~~~~~~l~~~~~~c~kd~is~~k~w~f~~~~s~~~~e~~~~~l~n~~~~~~~~~~lrlh~~ylind~~~hcqrk~~~~~  182 (757)
T KOG4368|consen  103 MNEFDNLLQPIIDTCTKDAISAGKNWMFSNAKSPPHCELMAGHLRNRITADGAHFELRLHLIYLINDVLHHCQRKQAREL  182 (757)
T ss_pred             HHHHHHHHHHHHHHHhHHHHHHhhhhhhhcCCCchHHHHHHHHHHhhhcccccchhhhhhhHHHHHHHHHHHHHHHHHHH
Confidence            34455555544  6899999999999999987   567777888888875  678899999999999999999885 578


Q ss_pred             HHHHHHHHHHHHHHhcccCCChHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHH
Q psy15160         78 GKEFGHVLKQAFVSVGDVHCSEKTRSSLSRILNIWEERGVYDKQQIASFRTAF  130 (366)
Q Consensus        78 ~~~F~~vL~~af~~i~~~~~d~~~~~kv~RIL~IW~eR~Vy~~~~i~~L~~~L  130 (366)
                      ..+.+.++..+.+.-. ....+.-.+++.|+|..|+.|++|+..++.+|++..
T Consensus       183 ~~~l~~~v~~~yc~~~-~~~~e~~~~~~~~ll~~we~~~yf~ds~~~ql~~~~  234 (757)
T KOG4368|consen  183 LAALQKVVVPIYCTSF-LAVEEDKQQKIARLLQLWEKNGYFDDSIIQQLQSPA  234 (757)
T ss_pred             HHHHHHHhHHHHHhhh-hhhHhHHHHHHHHHHHHHhhcCchhHHHHHHhhhhh
Confidence            8999998877776655 334556678999999999999999999999998643

>KOG2669|consensus

Probab=98.75  E-value=3.7e-08  Score=96.94  Aligned_cols=158  Identities=22%  Similarity=0.344  Sum_probs=116.4

Q ss_pred             ccccccccccCCccccccccchhchhhccccchhhHHHHHHHhhhhccCc-chhhcCCCcchhhHhhhhhhhhcccCCcH
Q psy15160        181 QAFVSVGDVHCSEKTRSSLSRILNIWEERGVYDKQQIASFRTAFNAALEP-QTKRRKLSESNTEVLYDVDELETSASSDA  259 (366)
Q Consensus       181 ~af~hva~~~~dek~~~~l~r~l~Iw~er~vye~~~i~~~~~~~~~~~~~-~~~~~k~p~~~~eli~~l~~~e~s~sSp~  259 (366)
                      .||.|+. ..++.+|++.++|+++||++|+||.+.++..+..++....+| -..+++.|+.-.++-....+.+.+++++.
T Consensus        87 ~a~~~i~-~~~~~~~k~~l~Rl~nIw~eR~Vf~~~~~~~l~~~l~~e~p~~~d~~~~~~~~~~~~k~~~~~~~~~~~~~~  165 (325)
T KOG2669|consen   87 KAFAHIV-EETDVKCKKKLGRLINIWEERNVFSPESLVDLEESLGAEKPPPLDEAKKLPRGSKQIKLDEKGSKPGLSSLG  165 (325)
T ss_pred             HHHHHHH-HhcchhhhHHHHHHHHHHHHhccCCHHHHHHHHHHhcccCCcchhhhhccccchHhhhhhhhccCCCCCCcc
Confidence            4788887 567889999999999999999999999999999988422222 11123334333333334556666777776


Q ss_pred             HHHHHhhcCCCCchhhhhhHhhhCCCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHH-HHHHHHHHH
Q psy15160        260 NIREKIAKLPPEVSEIQLLSKVQGKNITGQPDRVAAENLSIQVNEAVDLLTNYNTRLVTEMEDRKRASAM-LKDYIAAQR  338 (366)
Q Consensus       260 ~~r~~ia~lpPEveel~~L~~Led~~~~~~~~~~~~~~l~~~v~ea~~~l~~y~~rL~~e~~~r~~l~~~-L~~~~~~q~  338 (366)
                      .+.++|.+   -++.+++++++++.                 -..++..+.++.++|-.|+.+...+... |...+..+.
T Consensus       166 ~v~~~~~~---~~~l~~a~~s~~~~-----------------~~k~~~~~~~~i~~~~~e~~e~~~~~k~~~~~~~e~~~  225 (325)
T KOG2669|consen  166 EVHEKIDS---SVELVRALQSLENA-----------------ASKLDAVLEERIARLPQEVEEVSSLEKITLNSLIESLA  225 (325)
T ss_pred             ccchhHHh---HHHHHHHHHHHHHH-----------------HHHHhHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHH
Confidence            66442222   13344788888877                 4456788889999999999999988876 999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHH
Q psy15160        339 ELLEQAEQRLEVSETEIFLFL  359 (366)
Q Consensus       339 ~~~~~~~~~l~e~~~~~~~~~  359 (366)
                      -.+..++..|.+|...|..-.
T Consensus       226 k~lee~~~lL~e~~~~L~s~~  246 (325)
T KOG2669|consen  226 KHLEEEEMLLREVNPRLAAEE  246 (325)
T ss_pred             HHHHHHHHHHHHHHHHhcccc
Confidence            999999999999988876544

>KOG0132|consensus

Probab=98.56  E-value=1.2e-07  Score=100.81  Aligned_cols=123  Identities=19%  Similarity=0.390  Sum_probs=110.1

Q ss_pred             HHHHHHHHhccc-----cHHHHHHHHHHHhhhccchhHHHHHHHHHHhhcCcccchhHHHHhHHHHHHhhhc----Ccch
Q psy15160          7 SALISKLEELNA-----SQQSIQTLSLWLIHHRKHHSTIVKTWIDEVEKADDHRKLTLMYLANDVIQNSKKK----GPEY   77 (366)
Q Consensus         7 ~~l~~kL~~L~~-----Sq~SIqtlS~W~l~h~k~a~~IV~~w~~~L~ka~~~kKL~lLYLaNDVlQnskkk----g~~f   77 (366)
                      ..|..-|.+|..     |..-|+.+....|.|.+.+..||....++++++++.+||.-||+++.|+-.++..    ...|
T Consensus         5 ~~Fn~eL~SL~DsK~~IS~sKi~~ITkaAikaIk~ykhVVqsVeKfi~kCkpe~Kl~gLYVIDSIVRqsrhq~~~~kd~F   84 (894)
T KOG0132|consen    5 KEFNGELDSLEDSKPGISGSKILKITKAAIKAIKLYKHVVQSVEKFIKKCKPEYKLPGLYVIDSIVRQSRHQFGKEKDVF   84 (894)
T ss_pred             HHHHHHHHHhhccCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCcccccCeeEEehHHHHHHHHhhccccccc
Confidence            467788888864     5668999999999999999999999999999999999999999999999998853    2468


Q ss_pred             HHHHHHHHHHHHHHhcccCCChHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHH
Q psy15160         78 GKEFGHVLKQAFVSVGDVHCSEKTRSSLSRILNIWEERGVYDKQQIASFRTAFN  131 (366)
Q Consensus        78 ~~~F~~vL~~af~~i~~~~~d~~~~~kv~RIL~IW~eR~Vy~~~~i~~L~~~L~  131 (366)
                      ..-|..-+-..|..++  .|..+.+.++-|+|+.|..++||-.++|..|.++..
T Consensus        85 ~prf~~n~~~tf~~L~--~c~~edks~iIrvlNlwqkn~VfK~e~IqpLlDm~~  136 (894)
T KOG0132|consen   85 GPRFSKNFTGTFQNLY--ECPQEDKSDIIRVLNLWQKNNVFKSEIIQPLLDMAD  136 (894)
T ss_pred             CCccchhHHHHHHHHH--hcCHHHHHHHHHhhhhhhcccchhHHHHHHHHHHHh
Confidence            8889999999999999  346788999999999999999999999999999887

>KOG2071|consensus

Probab=97.63  E-value=0.00015  Score=76.31  Aligned_cols=121  Identities=23%  Similarity=0.389  Sum_probs=105.4

Q ss_pred             HHHHHHHHhcc-ccHHHHHHHHHHHhhhccchhHHHHHHHHHHhhcCcccchhHHHHhHHHHHHhhhcCcchHHHHHHHH
Q psy15160          7 SALISKLEELN-ASQQSIQTLSLWLIHHRKHHSTIVKTWIDEVEKADDHRKLTLMYLANDVIQNSKKKGPEYGKEFGHVL   85 (366)
Q Consensus         7 ~~l~~kL~~L~-~Sq~SIqtlS~W~l~h~k~a~~IV~~w~~~L~ka~~~kKL~lLYLaNDVlQnskkkg~~f~~~F~~vL   85 (366)
                      --+..-|-.|+ |+..-|.++..-.-+|...|..||..+..++.++++..||..||++..|+-|   -|.+|...|...|
T Consensus         7 ~dy~s~ledltfnskp~i~~lt~la~En~~~a~~iv~~iE~hi~kcpp~~kL~~~y~~dsi~kn---vg~py~~~fs~~l   83 (579)
T KOG2071|consen    7 RDYQSSLEDLTFNSKPIINTLTILAEENLPFAKSIVSAIEAHIAKCPPSQKLPVMYLLDSIVKN---VGSPYTTAFSRNL   83 (579)
T ss_pred             HHHHHHHHHHhcCCcchhHHhhHhhhhcccccHHHHHHHHHHHhhCCcccccchhhhhHHHHhh---cCCcchhhhhhhH
Confidence            34567788886 9999999999999999999999999999999999999999999999999966   4667999999999


Q ss_pred             HHHHHHhcccCCChHHHHHHHHHHHHhh-------hCCCCCHHHHHHHHHHHH
Q psy15160         86 KQAFVSVGDVHCSEKTRSSLSRILNIWE-------ERGVYDKQQIASFRTAFN  131 (366)
Q Consensus        86 ~~af~~i~~~~~d~~~~~kv~RIL~IW~-------eR~Vy~~~~i~~L~~~L~  131 (366)
                      ...|.+++ ...|+-.+.++.+++..|.       ---+|++-....+...+.
T Consensus        84 ~a~f~~~~-~~vd~r~r~~l~~~~~tw~~~~~~~sl~p~~~~~~~~~i~q~~~  135 (579)
T KOG2071|consen   84 VATFICAF-TKVDERTRTSLFKLRATWDLDPRSNSLDPAWSGVATSKIEQNLK  135 (579)
T ss_pred             HHHHHHHH-hhccccccchhHhhHHhhccCCCCCCCCccCCccchhhhhhhhh
Confidence            99999999 7889999999999999998       123456666777776665

>PF04818 CTD_bind: RNA polymerase II-binding domain

Probab=92.53  E-value=0.024  Score=42.85  Aligned_cols=32  Identities=34%  Similarity=0.700  Sum_probs=26.1

Q ss_pred             ccccccccccCCccccccccchhchhhccccch
Q psy15160        181 QAFVSVGDVHCSEKTRSSLSRILNIWEERGVYD  213 (366)
Q Consensus       181 ~af~hva~~~~dek~~~~l~r~l~Iw~er~vye  213 (366)
                      .+|.|++.. .|+++++.+.|+++||++|++|+
T Consensus        33 ~~~~~~~~~-~~~~~~~kv~rll~iW~~r~if~   64 (64)
T PF04818_consen   33 DAFAHAYKN-VDPEVRKKVQRLLNIWEERNIFS   64 (64)
T ss_dssp             HHHHHHCCC-S-HHHHHHHHHHHHHHHHCTSS-
T ss_pred             HHHHHHHhc-CCHHHHHHHHHHHHHhhCCCCCC
Confidence            478888744 49999999999999999999984

; InterPro: IPR006903 This entry represents a conserved region found in a number of uncharacterised eukaryotic proteins.; PDB: 2L0I_A 2KM4_A 3D9I_B 3D9N_B 3D9O_A 3D9P_B 3D9K_A 3D9M_A 3D9J_A 3D9L_A ....

>cd00197 VHS_ENTH_ANTH VHS, ENTH and ANTH domain superfamily; composed of proteins containing a VHS, ENTH or ANTH domain

Probab=92.19  E-value=1.2  Score=37.09  Aligned_cols=93  Identities=11%  Similarity=0.151  Sum_probs=67.3

Q ss_pred             cHHHHHHHHHHHhhhccchhHHHHHHHHHHhhcCcccchhHHHHhHHHHHHhhhcCcchHHHHHH--HHHHHHHHhcc--
Q psy15160         19 SQQSIQTLSLWLIHHRKHHSTIVKTWIDEVEKADDHRKLTLMYLANDVIQNSKKKGPEYGKEFGH--VLKQAFVSVGD--   94 (366)
Q Consensus        19 Sq~SIqtlS~W~l~h~k~a~~IV~~w~~~L~ka~~~kKL~lLYLaNDVlQnskkkg~~f~~~F~~--vL~~af~~i~~--   94 (366)
                      +...|..+..-+-.....+..+++.+.+.|...++..++.-|||+.-+++||-.   .|...|..  ++..++...+.  
T Consensus        17 ~~~~i~~i~d~~~~~~~~~~~~~~~l~kRl~~~~~~~~lkaL~lLe~lvkN~g~---~f~~~i~~~~~~~~l~~~~~~~~   93 (115)
T cd00197          17 DWPLIMEICDLINETNVGPKEAVDAIKKRINNKNPHVVLKALTLLEYCVKNCGE---RFHQEVASNDFAVELLKFDKSKL   93 (115)
T ss_pred             CHHHHHHHHHHHHCCCccHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHHccH---HHHHHHHHhHHHHHHHHhhcccc
Confidence            566677777766555567789999999999988999999999999999999643   44444433  33333332111  


Q ss_pred             --cCCChHHHHHHHHHHHHhhh
Q psy15160         95 --VHCSEKTRSSLSRILNIWEE  114 (366)
Q Consensus        95 --~~~d~~~~~kv~RIL~IW~e  114 (366)
                        ...+..++.++..++..|.+
T Consensus        94 ~~~~~~~~Vr~k~~~l~~~w~~  115 (115)
T cd00197          94 LGDDVSTNVREKAIELVQLWAS  115 (115)
T ss_pred             ccCCCChHHHHHHHHHHHHHhC
Confidence              23467889999999999963

The VHS domain is present in Vps27 (Vacuolar Protein Sorting), Hrs (Hepatocyte growth factor-regulated tyrosine kinase substrate) and STAM (Signal Transducing Adaptor Molecule). It is located at the N-termini of proteins involved in intracellular membrane trafficking. The epsin N-terminal homology (ENTH) domain is an evolutionarily conserved protein module found primarily in proteins that participate in clathrin-mediated endocytosis. A set of proteins previously designated as harboring an ENTH domain in fact contains a highly similar, yet unique module referred to as an AP180 N-terminal homology (ANTH) domain. VHS, ENTH and ANTH domains are structurally similar and are composed of a superhelix of eight alpha helices. ENTH adnd ANTH (E/ANTH) domains bind both inositol phospholipids and proteins and contribute to the nucleation and formation of clathrin coats on membra

>PF00790 VHS: VHS domain; InterPro: IPR002014 The VHS domain is a ~140 residues long domain, whose name is derived from its occurrence in VPS-27, Hrs and STAM

Probab=91.85  E-value=2.1  Score=37.21  Aligned_cols=108  Identities=13%  Similarity=0.177  Sum_probs=74.1

Q ss_pred             HHHHHHHHHHhhhccchhHHHHHHHHHHhhcCcccchhHHHHhHHHHHHhhhc-Ccch-HHHHHHHHHHHHHHhcccCCC
Q psy15160         21 QSIQTLSLWLIHHRKHHSTIVKTWIDEVEKADDHRKLTLMYLANDVIQNSKKK-GPEY-GKEFGHVLKQAFVSVGDVHCS   98 (366)
Q Consensus        21 ~SIqtlS~W~l~h~k~a~~IV~~w~~~L~ka~~~kKL~lLYLaNDVlQnskkk-g~~f-~~~F~~vL~~af~~i~~~~~d   98 (366)
                      ..|-.++.-+-.....+.+.+..+.+.|...+++..+.-|.|++-++.||-.. ..++ ...|-..|..++..-.   .+
T Consensus        24 ~~~l~icD~i~~~~~~~kea~~~l~krl~~~~~~vq~~aL~lld~lvkNcg~~f~~ev~~~~fl~~l~~l~~~~~---~~  100 (140)
T PF00790_consen   24 SLILEICDLINSSPDGAKEAARALRKRLKHGNPNVQLLALTLLDALVKNCGPRFHREVASKEFLDELVKLIKSKK---TD  100 (140)
T ss_dssp             HHHHHHHHHHHTSTTHHHHHHHHHHHHHTTSSHHHHHHHHHHHHHHHHHSHHHHHHHHTSHHHHHHHHHHHHHTT---TH
T ss_pred             HHHHHHHHHHHcCCccHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHcCCHHHHHHHhHHHHHHHHHHHHccCC---CC
Confidence            55666666555556678999999999999989999999999999999997533 2222 2234455544444333   22


Q ss_pred             hH--HHHHHHHHHHHhhh--CCCCCHHHHHHHHHHHH
Q psy15160         99 EK--TRSSLSRILNIWEE--RGVYDKQQIASFRTAFN  131 (366)
Q Consensus        99 ~~--~~~kv~RIL~IW~e--R~Vy~~~~i~~L~~~L~  131 (366)
                      +.  +++++..+|..|.+  ++...-..+..+...|.
T Consensus       101 ~~~~Vk~k~l~ll~~W~~~f~~~~~~~~i~~~y~~Lk  137 (140)
T PF00790_consen  101 PETPVKEKILELLQEWAEAFKSDPELSLIQDTYKRLK  137 (140)
T ss_dssp             HHSHHHHHHHHHHHHHHHHTTTSTTGHHHHHHHHHHH
T ss_pred             chhHHHHHHHHHHHHHHHHHCCCCCchHHHHHHHHHH
Confidence            33  89999999999997  44444555555555543

Based on regions surrounding the domain, VHS-proteins can be divided into 4 groups []: STAM/EAST/Hbp which all share the domain composition VHS-SH3-ITAM and carry one or two ubiquitin-interacting motifs Proteins with a FYVE domain (IPR000306 from INTERPRO) C-terminal to VHS which also carry one or two ubiquitin-interacting motifs GGA proteins with a domain composition VHS-GAT (GGA and Tom1) homology domain VHS domain alone or in combination with domains other than those listed above The VHS domain is always found at the N- terminus of proteins suggesting that such topology is important for function. The domain is considered to have a general membrane targeting/cargo recognition role in vesicular trafficking []. Resolution of the crystal structure of the VHS domain of Drosophila Hrs and human Tom1 revealed that it consists of eight helices arranged in a double-layer superhelix []. The existence of conserved patches of residues on the domain surface suggests that VHS domains may be involved in protein-protein recognition and docking. Overall, sequence similarity is low (approx 25%) amongst domain family members.; GO: 0006886 intracellular protein transport; PDB: 1X5B_A 2L0T_B 1DVP_A 3LDZ_C 3ZYQ_A 4AVX_A 3G2U_A 3G2W_A 1UJJ_A 3G2V_A ....

>cd03561 VHS VHS domain family; The VHS domain is present in Vps27 (Vacuolar Protein Sorting), Hrs (Hepatocyte growth factor-regulated tyrosine kinase substrate) and STAM (Signal Transducing Adaptor Molecule)

Probab=89.76  E-value=2  Score=37.15  Aligned_cols=94  Identities=12%  Similarity=0.113  Sum_probs=66.2

Q ss_pred             HHHHHHHHHHHhhhccchhHHHHHHHHHHhhcCcccchhHHHHhHHHHHHhhhc-CcchHHHHHHHHHHHHHHhccc-CC
Q psy15160         20 QQSIQTLSLWLIHHRKHHSTIVKTWIDEVEKADDHRKLTLMYLANDVIQNSKKK-GPEYGKEFGHVLKQAFVSVGDV-HC   97 (366)
Q Consensus        20 q~SIqtlS~W~l~h~k~a~~IV~~w~~~L~ka~~~kKL~lLYLaNDVlQnskkk-g~~f~~~F~~vL~~af~~i~~~-~~   97 (366)
                      -+.|-.+..-+-.....+...++.+.+.|...++...+.-|+|+.-++.||-.. ..++..  ...|.+++..+... ..
T Consensus        18 ~~~il~icd~I~~~~~~~k~a~raL~krl~~~n~~vql~AL~lLd~~vkNcg~~f~~~i~s--~~fl~~l~~l~~~~~~~   95 (133)
T cd03561          18 WALNLELCDLINLKPNGPKEAARAIRKKIKYGNPHVQLLALTLLELLVKNCGKPFHLQVAD--KEFLLELVKIAKNSPKY   95 (133)
T ss_pred             HHHHHHHHHHHhCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhCChHHHHHHhh--HHHHHHHHHHhCCCCCC
Confidence            345555555454445578999999999999888888999999999999997543 223333  12333444344322 45


Q ss_pred             ChHHHHHHHHHHHHhhhC
Q psy15160         98 SEKTRSSLSRILNIWEER  115 (366)
Q Consensus        98 d~~~~~kv~RIL~IW~eR  115 (366)
                      ++.++.++..++.-|.+.
T Consensus        96 ~~~Vk~kil~ll~~W~~~  113 (133)
T cd03561          96 DPKVREKALELILAWSES  113 (133)
T ss_pred             CHHHHHHHHHHHHHHHHH
Confidence            789999999999999873

It has a superhelical structure similar to that of the ARM (Armadillo) repeats and is present at the N-termini of proteins involved in intracellular membrane trafficking. There are four general groups of VHS domain containing proteins based on their association with other domains. The first group consists of proteins of the STAM/EAST/Hbp family which has the domain composition VHS-SH3-ITAM. The second consists of proteins with a FYVE domain C-terminal to VHS. The third consists of GGA proteins with a domain composition VHS-GAT (GGA and TOM)-GAE (gamma-adaptin ear) domain. The fourth consists of proteins with a VHS domain alone or with domains other than those mentioned above. In GGA proteins, VHS domains are involved in cargo recognition in trans-Golgi, thereby having a general me

>smart00582 RPR domain present in proteins, which are involved in regulation of nuclear pre-mRNA

Probab=86.81  E-value=0.19  Score=42.25  Aligned_cols=39  Identities=33%  Similarity=0.696  Sum_probs=31.1

Q ss_pred             cccccccccCCccccccccchhchhhccccchhhHHHHHH
Q psy15160        182 AFVSVGDVHCSEKTRSSLSRILNIWEERGVYDKQQIASFR  221 (366)
Q Consensus       182 af~hva~~~~dek~~~~l~r~l~Iw~er~vye~~~i~~~~  221 (366)
                      +|.|+.. ..+++.++.+.++++||++|++|.++++..++
T Consensus        82 ~~~~~~~-~~~~~~~~ki~kll~iW~~~~iF~~~~i~~L~  120 (121)
T smart00582       82 ALRDVLG-AANDETKKKIRRLLNIWEERGIFPPSVLRPLR  120 (121)
T ss_pred             HHHHHHH-hCCHHHHHHHHHHHHHHhcCCCCCHHHHHHhh
Confidence            5555553 23478899999999999999999999987764

>smart00288 VHS Domain present in VPS-27, Hrs and STAM

Probab=86.25  E-value=6.5  Score=34.03  Aligned_cols=91  Identities=14%  Similarity=0.176  Sum_probs=61.2

Q ss_pred             HHHHHHHHHHhhhccchhHHHHHHHHHHhhcCcccchhHHHHhHHHHHHhhhc-Ccch-HHHHHHHHHHHHHHhcccCCC
Q psy15160         21 QSIQTLSLWLIHHRKHHSTIVKTWIDEVEKADDHRKLTLMYLANDVIQNSKKK-GPEY-GKEFGHVLKQAFVSVGDVHCS   98 (366)
Q Consensus        21 ~SIqtlS~W~l~h~k~a~~IV~~w~~~L~ka~~~kKL~lLYLaNDVlQnskkk-g~~f-~~~F~~vL~~af~~i~~~~~d   98 (366)
                      +.|-.+..-+-.....+...+..+.+.|...++...+.-|-|+..++.||-.+ +.++ ...|-..|..++..   ....
T Consensus        19 ~~~l~icD~i~~~~~~~k~a~r~l~krl~~~n~~v~l~AL~lLe~~vkNcg~~f~~ev~s~~fl~~L~~l~~~---~~~~   95 (133)
T smart00288       19 ELILEICDLINSTPDGPKDAVRLLKKRLNNKNPHVALLALTLLDACVKNCGSKFHLEVASKEFLNELVKLIKP---KYPL   95 (133)
T ss_pred             HHHHHHHHHHhCCCccHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHCCHHHHHHHHhHHHHHHHHHHHcC---CCCc
Confidence            44444545444444567899999999999888888888899999999997433 2222 22344433333332   2223


Q ss_pred             hHHHHHHHHHHHHhhh
Q psy15160         99 EKTRSSLSRILNIWEE  114 (366)
Q Consensus        99 ~~~~~kv~RIL~IW~e  114 (366)
                      +.+++++..++.-|.+
T Consensus        96 ~~Vk~kil~li~~W~~  111 (133)
T smart00288       96 PLVKKRILELIQEWAD  111 (133)
T ss_pred             HHHHHHHHHHHHHHHH
Confidence            4499999999999987

Unpublished observations. Domain of unknown function.

>cd03567 VHS_GGA VHS domain family, GGA subfamily; GGA (Golgi-localized, Gamma-ear-containing, Arf-binding) comprise a subfamily of ubiquitously expressed, monomeric, motif-binding cargo/clathrin adaptor proteins

Probab=81.92  E-value=8  Score=34.04  Aligned_cols=92  Identities=15%  Similarity=0.214  Sum_probs=61.5

Q ss_pred             HHHHHHHHhhhccchhHHHHHHHHHHhhcCcccchhHHHHhHHHHHHhhhc-CcchH-HHHHHHHHHHHHHhcc-cCCCh
Q psy15160         23 IQTLSLWLIHHRKHHSTIVKTWIDEVEKADDHRKLTLMYLANDVIQNSKKK-GPEYG-KEFGHVLKQAFVSVGD-VHCSE   99 (366)
Q Consensus        23 IqtlS~W~l~h~k~a~~IV~~w~~~L~ka~~~kKL~lLYLaNDVlQnskkk-g~~f~-~~F~~vL~~af~~i~~-~~~d~   99 (366)
                      |-.+..-+-.....+...+..+.+.|...++...|.-|-|+.-+++||-.. +.++. ..|-.-|..++..-+. ...+.
T Consensus        22 ileicD~In~~~~~~k~a~rai~krl~~~n~~v~l~AL~LLe~~vkNCG~~fh~evas~~Fl~el~kl~~~k~~~~~~~~  101 (139)
T cd03567          22 IQAFCEQINKEPEGPQLAVRLLAHKIQSPQEKEALQALTVLEACMKNCGERFHSEVGKFRFLNELIKLVSPKYLGSRTSE  101 (139)
T ss_pred             HHHHHHHHHcCCccHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHcCHHHHHHHHhHHHHHHHHHHhccccCCCCCCH
Confidence            333444343334456788888999998777777888889999999998644 23332 4454445555533221 23568


Q ss_pred             HHHHHHHHHHHHhhh
Q psy15160        100 KTRSSLSRILNIWEE  114 (366)
Q Consensus       100 ~~~~kv~RIL~IW~e  114 (366)
                      .++.++..++..|.+
T Consensus       102 ~Vk~kil~li~~W~~  116 (139)
T cd03567         102 KVKTKIIELLYSWTL  116 (139)
T ss_pred             HHHHHHHHHHHHHHH
Confidence            999999999999996

The VHS domain has a superhelical structure similar to the structure of the ARM (Armadillo) repeats and is present at the N-termini of proteins. GGA proteins have a multidomain structure consisting of an N-terminal VHS domain linked by a short proline-rich linker to a GAT (GGA and TOM) domain, which is followed by a long flexible linker to the C-terminal appendage, GAE (gamma-adaptin ear) domain. The VHS domain of GGA proteins binds to the acidic-cluster dileucine (DxxLL) motif found on the cytoplasmic tails of cargo proteins trafficked between the trans-Golgi network and the endosomal system.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	366
4fu3_A	135	Cid Of Human Rprd1b Length = 135		1e-32
4hfg_A	135	Cid Of Human Rprd1b Length = 135		3e-32
4flb_A	132	Cid Of Human Rprd2 Length = 132		2e-19
4fla_A	152	Crystal Structure Of Human Rprd1b, Carboxy-Terminal		3e-13
2km4_A	142	Solution Structure Of Rtt103 Ctd Interacting Domain		5e-09

>pdb|4FU3|A Chain A, Cid Of Human Rprd1b Length = 135

Iteration: 1
 Score =  136 bits (343), Expect = 1e-32,   Method: Compositional matrix adjust.
 Identities = 70/135 (51%), Positives = 88/135 (65%), Gaps = 1/135 (0%)
Query: 2   AGFTQSALISKLEELNASQQSIQTLSLWLIHHRKHHSTIVKTWIDEVEKADDHRKLTLMY 61
           + F++SAL  KL EL+ SQQS+QTLSLWLIHHRKH   IV  W  E+ KA  +RKLT +Y
Sbjct: 2   SSFSESALEKKLSELSNSQQSVQTLSLWLIHHRKHAGPIVSVWHRELRKAKSNRKLTFLY 61
Query: 62  LANDVIQNSKKKGPEYGKEFGHVLKQAFVSVGDVHCSEKTRSSLSRILNIWEERGVYDKQ 121
           LANDVIQNSK+KGPE+ +EF  VL  AF  V      E  +  L R+LNIW+ER VY  +
Sbjct: 62  LANDVIQNSKRKGPEFTREFESVLVDAFSHVAR-EADEGCKKPLERLLNIWQERSVYGGE 120
Query: 122 QIASFRTAFNAALEP 136
            I   + +   +  P
Sbjct: 121 FIQQLKLSXEDSKSP 135

>pdb|4HFG|A Chain A, Cid Of Human Rprd1b Length = 135

Iteration: 1
 Score =  135 bits (341), Expect = 3e-32,   Method: Compositional matrix adjust.
 Identities = 69/135 (51%), Positives = 87/135 (64%), Gaps = 1/135 (0%)
Query: 2   AGFTQSALISKLEELNASQQSIQTLSLWLIHHRKHHSTIVKTWIDEVEKADDHRKLTLMY 61
           + F++SAL  KL EL+ SQ S+QTLSLWLIHHRKH   IV  W  E+ KA  +RKLT +Y
Sbjct: 2   SSFSESALEKKLSELSNSQHSVQTLSLWLIHHRKHAGPIVSVWHRELRKAKSNRKLTFLY 61
Query: 62  LANDVIQNSKKKGPEYGKEFGHVLKQAFVSVGDVHCSEKTRSSLSRILNIWEERGVYDKQ 121
           LANDVIQNSK+KGPE+ +EF  VL  AF  V      E  +  L R+LNIW+ER VY  +
Sbjct: 62  LANDVIQNSKRKGPEFTREFESVLVDAFSHVAR-EADEGCKKPLERLLNIWQERSVYGGE 120
Query: 122 QIASFRTAFNAALEP 136
            I   + +   +  P
Sbjct: 121 FIQQLKLSMEDSKSP 135

>pdb|4FLB|A Chain A, Cid Of Human Rprd2 Length = 132

Iteration: 1
 Score = 93.2 bits (230), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 53/134 (39%), Positives = 76/134 (56%), Gaps = 5/134 (3%)
Query: 2   AGFTQSALISKLEELNASQQSIQTLSLWLIHHRKHHSTIVKTWIDEVEKADDHRKLTLMY 61
           AG  +S+L  K + +  + +SIQ LS W I ++KHHSTIV  W+  + ++    +L L Y
Sbjct: 3   AGALESSLDRKFQSVTNTMESIQGLSSWCIENKKHHSTIVYHWMKWLRRSAYPHRLNLFY 62
Query: 62  LANDVIQNSKKKGPEYGKE-FGHVLKQAFVSVGDVHCSEKTRSSLSRILNIWEERGVYDK 120
           LANDVIQN K+K     +E F  VL +A   V D   S+    S+ RI  IWE+R VY +
Sbjct: 63  LANDVIQNCKRKNAIIFRESFADVLPEAAALVKDPSVSK----SVERIFKIWEDRNVYPE 118
Query: 121 QQIASFRTAFNAAL 134
           + I + R A +   
Sbjct: 119 EMIVALREALSTTF 132

>pdb|4FLA|A Chain A, Crystal Structure Of Human Rprd1b, Carboxy-Terminal Domain Length = 152

Iteration: 1
 Score = 72.4 bits (176), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 40/91 (43%), Positives = 57/91 (62%), Gaps = 8/91 (8%)
Query: 243 EVLYDVDELETSASSDANIREKIAKLPPEVSEIQLLSKVQGKNITGQPDRVAAENLSIQV 302
           E++  + +LE +AS DA +R+KIA LP EV ++ LL K+         D+ AAE LS  V
Sbjct: 26  ELIKALQDLENAASGDATVRQKIASLPQEVQDVSLLEKI--------TDKEAAERLSKTV 77
Query: 303 NEAVDLLTNYNTRLVTEMEDRKRASAMLKDY 333
           +EA  LL  YN RL  E+EDR++ + ML +Y
Sbjct: 78  DEACLLLAEYNGRLAAELEDRRQLARMLVEY 108

>pdb|2KM4|A Chain A, Solution Structure Of Rtt103 Ctd Interacting Domain Length = 142

Iteration: 1
 Score = 58.9 bits (141), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 38/136 (27%), Positives = 66/136 (48%), Gaps = 4/136 (2%)
Query: 3   GFTQSALISKLEELNASQQSIQTLSLWLIHHRKHHSTIVKTWIDEVEK--ADDHRKLTLM 60
            F+     +KL  L  SQ+SI + S WL+   +    + + W + + +   +  RKL  +
Sbjct: 2   AFSSEQFTTKLNTLEDSQESISSASKWLLLQYRDAPKVAEMWKEYMLRPSVNTRRKLLGL 61
Query: 61  YLANDVIQNSK-KKGPEYGKEFGHVLKQAFVSVGDVHCSEKTRSSLSRILNIWEERGVYD 119
           YL N V+Q +K +K  ++   FG V  +    +         +  LSR++NI +ER ++ 
Sbjct: 62  YLMNHVVQQAKGQKIIQFQDSFGKVAAEVLGRINQ-EFPRDLKKKLSRVVNILKERNIFS 120
Query: 120 KQQIASFRTAFNAALE 135
           KQ +     +  AALE
Sbjct: 121 KQVVNDIERSLAAALE 136

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	366
4fld_A	135	Regulation of nuclear PRE-mRNA domain-containing 1	1e-39
4fld_A	135	Regulation of nuclear PRE-mRNA domain-containing 1	5e-06
4flb_A	132	Regulation of nuclear PRE-mRNA domain-containing;	4e-39
4flb_A	132	Regulation of nuclear PRE-mRNA domain-containing;	1e-05
2km4_A	142	Regulator of TY1 transposition protein 103; CTD-in	2e-37
2km4_A	142	Regulator of TY1 transposition protein 103; CTD-in	1e-06
3d9j_A	145	RNA-binding protein 16; SCAF8, RNA polymerase II C	5e-25
3d9j_A	145	RNA-binding protein 16; SCAF8, RNA polymerase II C	2e-04
1sz9_A	144	PCF11 protein; RNA polymerase II CTD interacting d	1e-20
3clj_A	157	Protein NRD1; CTD-interacting domain, nucleus, pho	3e-10
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	6e-10

>4flb_A Regulation of nuclear PRE-mRNA domain-containing; structural genomics consortium, SGC, protein binding; 1.80A {Homo sapiens} Length = 132

 Score =  134 bits (339), Expect = 4e-39
 Identities = 51/135 (37%), Positives = 73/135 (54%), Gaps = 5/135 (3%)

Query: 1   MAGFTQSALISKLEELNASQQSIQTLSLWLIHHRKHHSTIVKTWIDEVEKADDHRKLTLM 60
            AG  +S+L  K + +  + +SIQ LS W I ++KHHSTIV  W+  + ++    +L L 
Sbjct: 2   SAGALESSLDRKFQSVTNTMESIQGLSSWCIENKKHHSTIVYHWMKWLRRSAYPHRLNLF 61

Query: 61  YLANDVIQNSK-KKGPEYGKEFGHVLKQAFVSVGDVHCSEKTRSSLSRILNIWEERGVYD 119
           YLANDVIQN K K    + + F  VL +A   V D         S+ RI  IWE+R VY 
Sbjct: 62  YLANDVIQNCKRKNAIIFRESFADVLPEAAALVKD----PSVSKSVERIFKIWEDRNVYP 117

Query: 120 KQQIASFRTAFNAAL 134
           ++ I + R A +   
Sbjct: 118 EEMIVALREALSTTF 132

>4flb_A Regulation of nuclear PRE-mRNA domain-containing; structural genomics consortium, SGC, protein binding; 1.80A {Homo sapiens} Length = 132

 Score = 43.4 bits (102), Expect = 1e-05
 Identities = 15/60 (25%), Positives = 26/60 (43%), Gaps = 4/60 (6%)

Query: 173 RRNKYDKKQAF----VSVGDVHCSEKTRSSLSRILNIWEERGVYDKQQIASFRTAFNAAL 228
           R+N    +++F         +        S+ RI  IWE+R VY ++ I + R A +   
Sbjct: 73  RKNAIIFRESFADVLPEAAALVKDPSVSKSVERIFKIWEDRNVYPEEMIVALREALSTTF 132

>2km4_A Regulator of TY1 transposition protein 103; CTD-interacting domain, RNA polymerase II binding protein, phosphoprotein; NMR {Saccharomyces cerevisiae} PDB: 2l0i_A* Length = 142

 Score =  130 bits (328), Expect = 2e-37
 Identities = 40/140 (28%), Positives = 67/140 (47%), Gaps = 5/140 (3%)

Query: 1   MAGFTQSALISKLEELNASQQSIQTLSLWLIHHRKHHSTIVKTWIDEV--EKADDHRKLT 58
           MA F+     +KL  L  SQ+SI + S WL+   +    + + W + +     +  RKL 
Sbjct: 1   MA-FSSEQFTTKLNTLEDSQESISSASKWLLLQYRDAPKVAEMWKEYMLRPSVNTRRKLL 59

Query: 59  LMYLANDVIQNSK-KKGPEYGKEFGHVLKQAFVSVGDVHCSEKTRSSLSRILNIWEERGV 117
            +YL N V+Q +K +K  ++   FG V  +    +         +  LSR++NI +ER +
Sbjct: 60  GLYLMNHVVQQAKGQKIIQFQDSFGKVAAEVLGRINQ-EFPRDLKKKLSRVVNILKERNI 118

Query: 118 YDKQQIASFRTAFNAALEPQ 137
           + KQ +     +  AALE  
Sbjct: 119 FSKQVVNDIERSLAAALEHH 138

>2km4_A Regulator of TY1 transposition protein 103; CTD-interacting domain, RNA polymerase II binding protein, phosphoprotein; NMR {Saccharomyces cerevisiae} PDB: 2l0i_A* Length = 142

 Score = 46.6 bits (110), Expect = 1e-06
 Identities = 13/42 (30%), Positives = 21/42 (50%)

Query: 190 HCSEKTRSSLSRILNIWEERGVYDKQQIASFRTAFNAALEPQ 231
                 +  LSR++NI +ER ++ KQ +     +  AALE  
Sbjct: 97  EFPRDLKKKLSRVVNILKERNIFSKQVVNDIERSLAAALEHH 138

>3d9j_A RNA-binding protein 16; SCAF8, RNA polymerase II CTD interacting domain, arm repeats phospho-CTD, phosphoprotein, transcription; 1.60A {Homo sapiens} PDB: 3d9k_A* 3d9l_A* 3d9m_A* 3d9n_A* 3d9p_A* 3d9i_A 3d9o_A* 2diw_A Length = 145

 Score = 97.9 bits (243), Expect = 5e-25
 Identities = 23/140 (16%), Positives = 57/140 (40%), Gaps = 11/140 (7%)

Query: 7   SALISKLEELNA-----SQQSIQTLSLWLIHHRKHHSTIVKTWIDEVEKADDHRKLTLMY 61
               S+L  LN      S+  +  ++   I   K +  +V++    ++K     K+  +Y
Sbjct: 5   KTFNSELYSLNDYKPPISKAKMTQITKAAIKAIKFYKHVVQSVEKFIQKCKPEYKVPGLY 64

Query: 62  LANDVIQNSKKKGPE----YGKEFGHVLKQAFVSVGDVHCSEKTRSSLSRILNIWEERGV 117
           + + +++ S+ +  +    +   F + +   F ++    C    +S + R+LN+W++  V
Sbjct: 65  VIDSIVRQSRHQFGQEKDVFAPRFSNNIISTFQNL--YRCPGDDKSKIVRVLNLWQKNNV 122

Query: 118 YDKQQIASFRTAFNAALEPQ 137
           +  + I        A     
Sbjct: 123 FKSEIIQPLLDMAAALEHHH 142

>3d9j_A RNA-binding protein 16; SCAF8, RNA polymerase II CTD interacting domain, arm repeats phospho-CTD, phosphoprotein, transcription; 1.60A {Homo sapiens} PDB: 3d9k_A* 3d9l_A* 3d9m_A* 3d9n_A* 3d9p_A* 3d9i_A 3d9o_A* 2diw_A Length = 145

 Score = 40.5 bits (94), Expect = 2e-04
 Identities = 9/42 (21%), Positives = 17/42 (40%)

Query: 190 HCSEKTRSSLSRILNIWEERGVYDKQQIASFRTAFNAALEPQ 231
            C    +S + R+LN+W++  V+  + I        A     
Sbjct: 101 RCPGDDKSKIVRVLNLWQKNNVFKSEIIQPLLDMAAALEHHH 142

>1sz9_A PCF11 protein; RNA polymerase II CTD interacting domain, arm repeats, transcription; 2.10A {Saccharomyces cerevisiae} SCOP: a.118.9.4 PDB: 1sza_A* 2bf0_X Length = 144

 Score = 85.9 bits (212), Expect = 1e-20
 Identities = 27/142 (19%), Positives = 45/142 (31%), Gaps = 13/142 (9%)

Query: 1   MAGFTQSAL---ISKLEELNA-SQQSIQTLSLWLIHHRKHHSTIVKTWIDEVEKADDHRK 56
           M   T+  +    S LEEL   S+  I TL+     +       V      +EK    +K
Sbjct: 1   MDHDTEVIVKDFNSILEELTFNSRPIITTLTKLAEENISCAQYFVDAIESRIEKCMPKQK 60

Query: 57  LTLMYLANDVIQNSKKKGPEYGKEFGHVLKQAFVSVGDVHCSEKTRSSLSRILNIWEERG 116
           L   Y  + + +N    G  Y   F   L   +           TR+ L  +  +W    
Sbjct: 61  LYAFYALDSICKNV---GSPYTIYFSRNLFNLYKRTYL-LVDNTTRTKLINMFKLWLNPN 116

Query: 117 -----VYDKQQIASFRTAFNAA 133
                +++   +         A
Sbjct: 117 DTGLPLFEGSALEKIEQFLIKA 138

>3clj_A Protein NRD1; CTD-interacting domain, nucleus, phosphoprotein, RNA polymer binding protein, RNA binding protein; 2.10A {Saccharomyces cerevisiae} Length = 157

 Score = 57.1 bits (137), Expect = 3e-10
 Identities = 23/130 (17%), Positives = 49/130 (37%), Gaps = 13/130 (10%)

Query: 17  NASQQSIQTLSLWLIHHRKHHSTIVKTWIDEVEKADDHRKLTLMYLANDVIQNSK---KK 73
             S   I+ L+ + + H    S I+   ID      D  KL  +Y+ + + +      + 
Sbjct: 19  GISGSRIKKLTTYALDHIDIESKIISLIIDYSRLCPDSHKLGSLYIIDSIGRAYLDETRS 78

Query: 74  GPEYGKEFGHVLKQAFVSVGDV----------HCSEKTRSSLSRILNIWEERGVYDKQQI 123
                         A  ++G+V            ++  +  +  +L+IW+  G++ K  +
Sbjct: 79  NSNSSSNKPGTCAHAINTLGEVIQELLSDAIAKSNQDHKEKIRMLLDIWDRSGLFQKSYL 138

Query: 124 ASFRTAFNAA 133
            + R+   AA
Sbjct: 139 NAIRSKCFAA 148

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 59.9 bits (144), Expect = 6e-10
 Identities = 45/376 (11%), Positives = 111/376 (29%), Gaps = 100/376 (26%)

Query: 10  ISKLEELNASQQSIQTLSLWLIHHRKHHSTIVKTWIDEVEKADDHRKLTL--M------Y 61
           I + + L    Q     ++     R      ++  +    +    + + +  +      +
Sbjct: 113 IEQRDRLYNDNQVFAKYNVS----RLQPYLKLRQAL---LELRPAKNVLIDGVLGSGKTW 165

Query: 62  LANDVIQNSKKKGPEYGKEFGHVLKQAFVSVGDVHCSEKTRSSLSRILNIWEERGVYDKQ 121
           +A DV  + K +     K F       ++++ + +  E     L ++L   +        
Sbjct: 166 VALDVCLSYKVQCKMDFKIF-------WLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSD 218

Query: 122 QIASFRTAFNAALEPQTKRRKL--SESNTEVLYDVDGNVPIGYFTFFHIDGKGRRNKYDK 179
             ++ +   ++    Q + R+L  S+     L  +  NV                   + 
Sbjct: 219 HSSNIKLRIHSI---QAELRRLLKSKPYENCLLVLL-NV------------------QNA 256

Query: 180 K--QAFVSVGDVHCSEKTRSSLSRILNIWEERGVYDKQQIASFRTAFNAALEPQTKRRKL 237
           K   AF    ++ C         +IL     + V D              L   T     
Sbjct: 257 KAWNAF----NLSC---------KILLTTRFKQVTD-------------FLSAATTTHIS 290

Query: 238 SESNTEVLYDVDELETSASSDANIREKIAKLPPEVSEIQ-LLSKVQGKNITGQPDR---- 292
            + ++  L   +           +  +   LP EV         +  ++I          
Sbjct: 291 LDHHSMTLTPDEVKSLLLK---YLDCRPQDLPREVLTTNPRRLSIIAESIRDGLATWDNW 347

Query: 293 --VAAENLSIQVNEAVDLLTNYNTRLVTEMEDRKRASAMLKD--YIAAQRELLEQAEQRL 348
             V  + L+  +  ++++L         E        ++     +I     LL      +
Sbjct: 348 KHVNCDKLTTIIESSLNVLEPA------EYRKMFDRLSVFPPSAHIPTI--LLS----LI 395

Query: 349 --EVSETEIFLFLKKF 362
             +V ++++ + + K 
Sbjct: 396 WFDVIKSDVMVVVNKL 411

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	366
2km4_A	142	Regulator of TY1 transposition protein 103; CTD-in	100.0
4fu3_A	135	Regulation of nuclear PRE-mRNA domain-containing 1	100.0
4flb_A	132	Regulation of nuclear PRE-mRNA domain-containing;	100.0
4fla_A	152	Regulation of nuclear PRE-mRNA domain-containing 1	99.95
3d9j_A	145	RNA-binding protein 16; SCAF8, RNA polymerase II C	99.95
1sz9_A	144	PCF11 protein; RNA polymerase II CTD interacting d	99.93
3clj_A	157	Protein NRD1; CTD-interacting domain, nucleus, pho	99.58
4fu3_A	135	Regulation of nuclear PRE-mRNA domain-containing 1	95.61
4flb_A	132	Regulation of nuclear PRE-mRNA domain-containing;	95.6
2km4_A	142	Regulator of TY1 transposition protein 103; CTD-in	95.39
3d9j_A	145	RNA-binding protein 16; SCAF8, RNA polymerase II C	94.21
1x5b_A	163	Signal transducing adaptor molecule 2; VHS domain,	93.37
1sz9_A	144	PCF11 protein; RNA polymerase II CTD interacting d	91.83
4fla_A	152	Regulation of nuclear PRE-mRNA domain-containing 1	84.46

>2km4_A Regulator of TY1 transposition protein 103; CTD-interacting domain, RNA polymerase II binding protein, phosphoprotein; NMR {Saccharomyces cerevisiae} PDB: 2l0i_A*

Probab=100.00  E-value=3.3e-37  Score=269.01  Aligned_cols=131  Identities=27%  Similarity=0.500  Sum_probs=124.1

Q ss_pred             CCCCHHHHHHHHHhccccHHHHHHHHHHHhhhccchhHHHHHHHHHHhhc--CcccchhHHHHhHHHHHHhhhc-CcchH
Q psy15160          2 AGFTQSALISKLEELNASQQSIQTLSLWLIHHRKHHSTIVKTWIDEVEKA--DDHRKLTLMYLANDVIQNSKKK-GPEYG   78 (366)
Q Consensus         2 ~~Fse~~l~~kL~~L~~Sq~SIqtlS~W~l~h~k~a~~IV~~w~~~L~ka--~~~kKL~lLYLaNDVlQnskkk-g~~f~   78 (366)
                      |+||+++|.++|++||+||+|||++|.|||+|+++++.||++|.++|.++  ++++||++|||||||+|||+++ +++|+
T Consensus         1 m~fs~~~l~~kL~~L~~sq~sIq~~s~W~l~h~~~a~~iv~~~~~~l~~~~~~~~kKL~~lYL~NDVlqnsk~k~~~~f~   80 (142)
T 2km4_A            1 MAFSSEQFTTKLNTLEDSQESISSASKWLLLQYRDAPKVAEMWKEYMLRPSVNTRRKLLGLYLMNHVVQQAKGQKIIQFQ   80 (142)
T ss_dssp             -CCCHHHHHHHHHTCCSCHHHHHHHHHHHHTCGGGHHHHHHHHHHHHTSSSSCHHHHHHHHHHHHHHHHHHGGGTCCHHH
T ss_pred             CCCCHHHHHHHHHhccccHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHhcCCCccceehhhhhHHHHHHHHhhcCchHHH
Confidence            79999999999999999999999999999999999999999999999986  7799999999999999999986 68999


Q ss_pred             HHHHHHHHHHHHHhcccCCChHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHhh
Q psy15160         79 KEFGHVLKQAFVSVGDVHCSEKTRSSLSRILNIWEERGVYDKQQIASFRTAFNAA  133 (366)
Q Consensus        79 ~~F~~vL~~af~~i~~~~~d~~~~~kv~RIL~IW~eR~Vy~~~~i~~L~~~L~~~  133 (366)
                      .+|+++||++|.+++ ...+++.+++|.|||+||++|+||++++|.+|+..+.+.
T Consensus        81 ~~F~~~L~~~~~~~~-~~~~~~~~~kv~rvl~iWeer~vf~~~~i~~L~~~l~~~  134 (142)
T 2km4_A           81 DSFGKVAAEVLGRIN-QEFPRDLKKKLSRVVNILKERNIFSKQVVNDIERSLAAA  134 (142)
T ss_dssp             HHHHHTHHHHHHHHH-HHSCHHHHHHHHHHHHHHHHHTCSCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHH-HcCCHHHHHHHHHHHHHhhccCCcCHHHHHHHHHHHHhH
Confidence            999999999999999 456899999999999999999999999999999998743

>4fu3_A Regulation of nuclear PRE-mRNA domain-containing 1B; structural genomics consortium, SGC, domain swapping, transc; HET: MSE; 1.90A {Homo sapiens} PDB: 4fld_A*

Probab=100.00  E-value=7e-36  Score=256.91  Aligned_cols=129  Identities=53%  Similarity=0.866  Sum_probs=123.5

Q ss_pred             CCCCHHHHHHHHHhccccHHHHHHHHHHHhhhccchhHHHHHHHHHHhhcCcccchhHHHHhHHHHHHhhhcCcchHHHH
Q psy15160          2 AGFTQSALISKLEELNASQQSIQTLSLWLIHHRKHHSTIVKTWIDEVEKADDHRKLTLMYLANDVIQNSKKKGPEYGKEF   81 (366)
Q Consensus         2 ~~Fse~~l~~kL~~L~~Sq~SIqtlS~W~l~h~k~a~~IV~~w~~~L~ka~~~kKL~lLYLaNDVlQnskkkg~~f~~~F   81 (366)
                      |+|++++|.++|++||+||+||++++.||++|++++..||++|.++|.++++++||++|||+|||+|||+++|++|+.+|
T Consensus         2 ssf~~~~l~~~L~~L~~s~~sI~~~s~w~l~~~~~a~~iv~~i~~~l~~~~~~~KL~~LYLindIl~ns~~~~~~y~~~f   81 (135)
T 4fu3_A            2 SSFSESALEKKLSELSNSQQSVQTLSLWLIHHRKHAGPIVSVWHRELRKAKSNRKLTFLYLANDVIQNSKRKGPEFTREF   81 (135)
T ss_dssp             -CCCHHHHHHHHHHCCSSTTHHHHHHHHHHHTGGGHHHHHHHHHHHHHHSCTTTHHHHHHHHHHHHHHHTTTCSHHHHHH
T ss_pred             CCCCHHHHHHHHHHccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccchhHHHHHHHHHHHHHHHhcCHHHHHHH
Confidence            79999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHhcccCCChHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHH
Q psy15160         82 GHVLKQAFVSVGDVHCSEKTRSSLSRILNIWEERGVYDKQQIASFRTAFN  131 (366)
Q Consensus        82 ~~vL~~af~~i~~~~~d~~~~~kv~RIL~IW~eR~Vy~~~~i~~L~~~L~  131 (366)
                      +++||.+|.+++ ...+++++++|.|||++|++|+||++++|.+|+..|.
T Consensus        82 ~~~l~~~~~~~~-~~~~~~~k~kl~kll~iW~~r~vf~~~~i~~L~~~l~  130 (135)
T 4fu3_A           82 ESVLVDAFSHVA-READEGCKKPLERLLNIWQERSVYGGEFIQQLKLSME  130 (135)
T ss_dssp             HTTHHHHHHHHH-HHHHTTSSHHHHHHHHHHHHTTSSCHHHHHHHHHTC-
T ss_pred             HHHHHHHHHHHH-HcCCHHHHHHHHHHHHHhcCCCCcCHHHHHHHHHHHh
Confidence            999999999999 4557789999999999999999999999999999886

>4flb_A Regulation of nuclear PRE-mRNA domain-containing; structural genomics consortium, SGC, protein binding; 1.80A {Homo sapiens}

Probab=100.00  E-value=7.2e-34  Score=243.87  Aligned_cols=127  Identities=39%  Similarity=0.641  Sum_probs=121.5

Q ss_pred             CCCCCHHHHHHHHHhccccHHHHHHHHHHHhhhccchhHHHHHHHHHHhhcCcccchhHHHHhHHHHHHhhhcC-cchHH
Q psy15160          1 MAGFTQSALISKLEELNASQQSIQTLSLWLIHHRKHHSTIVKTWIDEVEKADDHRKLTLMYLANDVIQNSKKKG-PEYGK   79 (366)
Q Consensus         1 M~~Fse~~l~~kL~~L~~Sq~SIqtlS~W~l~h~k~a~~IV~~w~~~L~ka~~~kKL~lLYLaNDVlQnskkkg-~~f~~   79 (366)
                      +++|.+++|.++|++||+||+||++++.|||+|++++..||++|.++|.++++++||++|||+|||+|||++++ +.|..
T Consensus         2 ~~~~~e~~l~~~L~~L~~s~~sI~~~s~w~l~h~~~a~~Iv~~i~~~l~~~~~~~KL~~LYL~ndIl~ns~~~~~~~f~~   81 (132)
T 4flb_A            2 SAGALESSLDRKFQSVTNTMESIQGLSSWCIENKKHHSTIVYHWMKWLRRSAYPHRLNLFYLANDVIQNCKRKNAIIFRE   81 (132)
T ss_dssp             CHHHHHHHHHHHHHHCCSSHHHHHHHHHHHHHTGGGHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHTTTTTCTHHHH
T ss_pred             CchHHHHHHHHHHHHCcccHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHcCChhhHHHHHHHHHHHHHHhcccChHHHHH
Confidence            36789999999999999999999999999999999999999999999999999999999999999999999885 68999


Q ss_pred             HHHHHHHHHHHHhcccCCChHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHH
Q psy15160         80 EFGHVLKQAFVSVGDVHCSEKTRSSLSRILNIWEERGVYDKQQIASFRTAFN  131 (366)
Q Consensus        80 ~F~~vL~~af~~i~~~~~d~~~~~kv~RIL~IW~eR~Vy~~~~i~~L~~~L~  131 (366)
                      .|+++||.+|.+++    +++.+++|.|||++|++|+||++++|.+|+..|.
T Consensus        82 ~f~~~l~~~~~~~~----~~~~~~kl~~ll~iW~~r~vf~~~~i~~L~~~L~  129 (132)
T 4flb_A           82 SFADVLPEAAALVK----DPSVSKSVERIFKIWEDRNVYPEEMIVALREALS  129 (132)
T ss_dssp             HHHTTHHHHHHTTC----STTTHHHHHHHHHHHHHHTSSCHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHhC----CHHHHHHHHHHHHHhccCCCcCHHHHHHHHHHHh
Confidence            99999999999887    6788999999999999999999999999999996

>4fla_A Regulation of nuclear PRE-mRNA domain-containing 1B; structural genomics consortium, SGC, transcription; 2.20A {Homo sapiens}

Probab=99.95  E-value=1.1e-28  Score=217.44  Aligned_cols=121  Identities=37%  Similarity=0.534  Sum_probs=109.7

Q ss_pred             cchhhcCCCcchhhHhhhhhhhhcccCCcHHHHHHhhcCCCCchhhhhhHhhhCCCCCCCCcHHHHHHHHHHHHHHHHHH
Q psy15160        230 PQTKRRKLSESNTEVLYDVDELETSASSDANIREKIAKLPPEVSEIQLLSKVQGKNITGQPDRVAAENLSIQVNEAVDLL  309 (366)
Q Consensus       230 ~~~~~~k~p~~~~eli~~l~~~e~s~sSp~~~r~~ia~lpPEveel~~L~~Led~~~~~~~~~~~~~~l~~~v~ea~~~l  309 (366)
                      +.-+.+.||. +++||+.++++++++|||+.+|++||+|||||+|+++|++|+|+        ++|++|+++|++||++|
T Consensus        14 ~~~~~~~p~~-~~elik~L~~le~sassDa~vrq~Ia~LP~eVsd~s~l~klkDk--------~~~e~l~~~veeA~~~L   84 (152)
T 4fla_A           14 LYFQGAGPLL-TEELIKALQDLENAASGDATVRQKIASLPQEVQDVSLLEKITDK--------EAAERLSKTVDEACLLL   84 (152)
T ss_dssp             ---------C-HHHHHHHHHHHHHHHHHHHHHHHHHHTSCGGGTCGGGGGGCCSH--------HHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCC-HHHHHHHHHHhhccccchHHHHHHHHcCCccccCHHHHHHcccH--------HHHHHHHHHHHHHHHHH
Confidence            3333344454 89999999999999999999999999999999999999999999        99999999999999999


Q ss_pred             HHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy15160        310 TNYNTRLVTEMEDRKRASAMLKDYIAAQRELLEQAEQRLEVSETEIFLFL  359 (366)
Q Consensus       310 ~~y~~rL~~e~~~r~~l~~~L~~~~~~q~~~~~~~~~~l~e~~~~~~~~~  359 (366)
                      ++||+||++||++|++|++||++|+..|++.+++++++|++|+.++.++.
T Consensus        85 ~eYn~rL~~E~~dR~~L~~~L~~~~~~~~~~l~e~e~~leeyK~Kl~rv~  134 (152)
T 4fla_A           85 AEYNGRLAAELEDRRQLARMLVEYTQNQKDVLSEKEKKLEEYKQKLARVT  134 (152)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            99999999999999999999999999999999999999999999998875

>3d9j_A RNA-binding protein 16; SCAF8, RNA polymerase II CTD interacting domain, arm repeats phospho-CTD, phosphoprotein, transcription; 1.60A {Homo sapiens} PDB: 3d9k_A* 3d9l_A* 3d9m_A* 3d9n_A* 3d9p_A* 3d9i_A 3d9o_A* 2diw_A

Probab=99.95  E-value=4.4e-27  Score=205.82  Aligned_cols=124  Identities=17%  Similarity=0.325  Sum_probs=117.3

Q ss_pred             HHHHHHHHHhc-----cccHHHHHHHHHHHhhhccchhHHHHHHHHHHhhcCcccchhHHHHhHHHHHHhhhcCc----c
Q psy15160          6 QSALISKLEEL-----NASQQSIQTLSLWLIHHRKHHSTIVKTWIDEVEKADDHRKLTLMYLANDVIQNSKKKGP----E   76 (366)
Q Consensus         6 e~~l~~kL~~L-----~~Sq~SIqtlS~W~l~h~k~a~~IV~~w~~~L~ka~~~kKL~lLYLaNDVlQnskkkg~----~   76 (366)
                      -+.|+.+|++|     ++|+.+|++++.||++|++++..||++|.++++++++.+||.+|||+|||+||++++++    .
T Consensus         4 v~~f~~~L~~L~~~k~~~S~~~I~~LT~~a~~~~~~~~~IV~~~~~~i~k~~~~~KL~~LYL~DsIvrn~~~k~~~~~~~   83 (145)
T 3d9j_A            4 VKTFNSELYSLNDYKPPISKAKMTQITKAAIKAIKFYKHVVQSVEKFIQKCKPEYKVPGLYVIDSIVRQSRHQFGQEKDV   83 (145)
T ss_dssp             HHHHHHHHHGGGGSCSSCCHHHHHHHHHHHHHTGGGHHHHHHHHHHHHHHSCGGGHHHHHHHHHHHHHHHHHHHCTTTCS
T ss_pred             HHHHHHHHHHHHhccCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCccceeehhhhhHHHHHHhhhhcCCcccc
Confidence            47899999999     67899999999999999999999999999999999999999999999999999998743    7


Q ss_pred             hHHHHHHHHHHHHHHhcccCCChHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHH
Q psy15160         77 YGKEFGHVLKQAFVSVGDVHCSEKTRSSLSRILNIWEERGVYDKQQIASFRTAFN  131 (366)
Q Consensus        77 f~~~F~~vL~~af~~i~~~~~d~~~~~kv~RIL~IW~eR~Vy~~~~i~~L~~~L~  131 (366)
                      |...|+++|+.+|.+++ . .+++++.++.|||+||++|+||++++|..|+..+.
T Consensus        84 f~~~F~~~L~~~f~~~~-~-~~~~~r~kl~rLl~iW~~r~vF~~~~l~~l~~~l~  136 (145)
T 3d9j_A           84 FAPRFSNNIISTFQNLY-R-CPGDDKSKIVRVLNLWQKNNVFKSEIIQPLLDMAA  136 (145)
T ss_dssp             HHHHHHHHHHHHHHHHT-S-SCGGGHHHHHHHHHHHHHTTSSCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHH-h-CCHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhc
Confidence            99999999999999999 3 45899999999999999999999999999999996

>1sz9_A PCF11 protein; RNA polymerase II CTD interacting domain, arm repeats, transcription; 2.10A {Saccharomyces cerevisiae} SCOP: a.118.9.4 PDB: 1sza_A* 2bf0_X

Probab=99.93  E-value=5.5e-26  Score=198.77  Aligned_cols=121  Identities=20%  Similarity=0.282  Sum_probs=116.3

Q ss_pred             HHHHHHHHhcc-ccHHHHHHHHHHHhhhccchhHHHHHHHHHHhhcCcccchhHHHHhHHHHHHhhhcCcchHHHHHHHH
Q psy15160          7 SALISKLEELN-ASQQSIQTLSLWLIHHRKHHSTIVKTWIDEVEKADDHRKLTLMYLANDVIQNSKKKGPEYGKEFGHVL   85 (366)
Q Consensus         7 ~~l~~kL~~L~-~Sq~SIqtlS~W~l~h~k~a~~IV~~w~~~L~ka~~~kKL~lLYLaNDVlQnskkkg~~f~~~F~~vL   85 (366)
                      +.|.++|++|+ +|+.+|++++.||++|++++..||++|.+++.++++.+||.+|||+|||++|+   |++|...|+++|
T Consensus        10 ~~f~~~L~~L~~nSk~~I~~LT~~a~~~~~~a~~Iv~~i~~~i~k~~p~~KL~~LYL~DsIvkN~---g~~y~~~F~~~l   86 (144)
T 1sz9_A           10 KDFNSILEELTFNSRPIITTLTKLAEENISCAQYFVDAIESRIEKCMPKQKLYAFYALDSICKNV---GSPYTIYFSRNL   86 (144)
T ss_dssp             HHHHHHHTTCSSCCHHHHHHHHHHHHHTGGGHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHT---CTTHHHHHHTTH
T ss_pred             HHHHHHHHHhccccHhHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCHhhHHHHHHHHHHHHHhc---cchHHHHHHHHH
Confidence            57899999999 99999999999999999999999999999999999999999999999999996   467999999999


Q ss_pred             HHHHHHhcccCCChHHHHHHHHHHHHhhhC-----CCCCHHHHHHHHHHHH
Q psy15160         86 KQAFVSVGDVHCSEKTRSSLSRILNIWEER-----GVYDKQQIASFRTAFN  131 (366)
Q Consensus        86 ~~af~~i~~~~~d~~~~~kv~RIL~IW~eR-----~Vy~~~~i~~L~~~L~  131 (366)
                      +++|.+++ ...|+.++.+|.||+++|++|     +||+++++..|+..|.
T Consensus        87 ~~~f~~~~-~~~d~~~r~k~~rL~~~W~~~~~~~~~vF~~~~l~~i~~~l~  136 (144)
T 1sz9_A           87 FNLYKRTY-LLVDNTTRTKLINMFKLWLNPNDTGLPLFEGSALEKIEQFLI  136 (144)
T ss_dssp             HHHHHHHH-HTSCHHHHHHHHHHHHHHTSGGGCSSCSSCHHHHHHHHHHHH
T ss_pred             HHHHHHHH-HhCCHHHHHHHHHHHHHHhCcccCCCCCCCHHHHHHHHHHHH
Confidence            99999999 567999999999999999999     9999999999999997

>3clj_A Protein NRD1; CTD-interacting domain, nucleus, phosphoprotein, RNA polymer binding protein, RNA binding protein; 2.10A {Saccharomyces cerevisiae}

Probab=99.58  E-value=4.9e-15  Score=130.94  Aligned_cols=126  Identities=18%  Similarity=0.356  Sum_probs=112.8

Q ss_pred             HHHHHHHHHhc-----cccHHHHHHHHHHHhhhccchhHHHHHHHHHHhhcCcccchhHHHHhHHHHHHhhh---c-C--
Q psy15160          6 QSALISKLEEL-----NASQQSIQTLSLWLIHHRKHHSTIVKTWIDEVEKADDHRKLTLMYLANDVIQNSKK---K-G--   74 (366)
Q Consensus         6 e~~l~~kL~~L-----~~Sq~SIqtlS~W~l~h~k~a~~IV~~w~~~L~ka~~~kKL~lLYLaNDVlQnskk---k-g--   74 (366)
                      -+.|+.-|++|     -.|..-|.++..||++|.+++..||+++.++++++++.+||..||+++.|+.+++.   + |  
T Consensus         3 v~ef~~~L~sL~~lkp~iS~skI~~LT~~A~~nv~~~~~iv~~l~~~ikk~p~~hKL~~LYVvDSIvR~~~~~~~k~g~~   82 (157)
T 3clj_A            3 FQNFVATLESFKDLKSGISGSRIKKLTTYALDHIDIESKIISLIIDYSRLCPDSHKLGSLYIIDSIGRAYLDETRSNSNS   82 (157)
T ss_dssp             HHHHHHHHHGGGGCSSSCCHHHHHHHHHHHHHTGGGHHHHHHHHHHHHHHSCGGGHHHHHHHHHHHHHHHHHHHHTCCC-
T ss_pred             HHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHhCCCcceeeeeeehHHHHHHHHHHHHhcCCc
Confidence            78899999988     57889999999999999999999999999999999999999999999999999873   1 2  


Q ss_pred             -----cch---HHHHHHHHHHHHHHhcccCCChHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHh
Q psy15160         75 -----PEY---GKEFGHVLKQAFVSVGDVHCSEKTRSSLSRILNIWEERGVYDKQQIASFRTAFNA  132 (366)
Q Consensus        75 -----~~f---~~~F~~vL~~af~~i~~~~~d~~~~~kv~RIL~IW~eR~Vy~~~~i~~L~~~L~~  132 (366)
                           ..|   +.-|...++..|..++ ...+++.+.++.++|+||+.+++|++++|..|++.+..
T Consensus        83 ~~a~~gt~a~~v~~~~e~i~~l~~~~~-~~~~~~~k~Ki~klldiW~k~~~Fp~e~i~~i~~~~~~  147 (157)
T 3clj_A           83 SSNKPGTCAHAINTLGEVIQELLSDAI-AKSNQDHKEKIRMLLDIWDRSGLFQKSYLNAIRSKCFA  147 (157)
T ss_dssp             ---STTSHHHHHHHHHHHHHHHHHHHH-HHSCHHHHHHHHHHHHHHHHHTTTTTSCCTTTTSHHHH
T ss_pred             cCCCCccHHHHHHHHHHHHHHHHHHHH-HcCCHHHHHHHHHHHHHHccCCCCCHHHHHHHHHHhhh
Confidence                 236   4567889999999988 45689999999999999999999999999999988863

>4fu3_A Regulation of nuclear PRE-mRNA domain-containing 1B; structural genomics consortium, SGC, domain swapping, transc; HET: MSE; 1.90A {Homo sapiens} PDB: 4fld_A*

Probab=95.61  E-value=0.0013  Score=55.54  Aligned_cols=45  Identities=33%  Similarity=0.648  Sum_probs=37.6

Q ss_pred             ccccccccccCCccccccccchhchhhccccchhhHHHHHHHhhhh
Q psy15160        181 QAFVSVGDVHCSEKTRSSLSRILNIWEERGVYDKQQIASFRTAFNA  226 (366)
Q Consensus       181 ~af~hva~~~~dek~~~~l~r~l~Iw~er~vye~~~i~~~~~~~~~  226 (366)
                      .+|.|++. ..++++++.+.|+++||++|++|+++++++++.++..
T Consensus        87 ~~~~~~~~-~~~~~~k~kl~kll~iW~~r~vf~~~~i~~L~~~l~~  131 (135)
T 4fu3_A           87 DAFSHVAR-EADEGCKKPLERLLNIWQERSVYGGEFIQQLKLSMED  131 (135)
T ss_dssp             HHHHHHHH-HHHTTSSHHHHHHHHHHHHTTSSCHHHHHHHHHTC--
T ss_pred             HHHHHHHH-cCCHHHHHHHHHHHHHhcCCCCcCHHHHHHHHHHHhC
Confidence            46777763 4578899999999999999999999999999988843

>4flb_A Regulation of nuclear PRE-mRNA domain-containing; structural genomics consortium, SGC, protein binding; 1.80A {Homo sapiens}

Probab=95.60  E-value=0.0031  Score=53.04  Aligned_cols=40  Identities=35%  Similarity=0.627  Sum_probs=35.2

Q ss_pred             cccccccccCCccccccccchhchhhccccchhhHHHHHHHhhh
Q psy15160        182 AFVSVGDVHCSEKTRSSLSRILNIWEERGVYDKQQIASFRTAFN  225 (366)
Q Consensus       182 af~hva~~~~dek~~~~l~r~l~Iw~er~vye~~~i~~~~~~~~  225 (366)
                      +|.|++    |+++++.+.|+++||++|++|+++++++++.+++
T Consensus        90 ~~~~~~----~~~~~~kl~~ll~iW~~r~vf~~~~i~~L~~~L~  129 (132)
T 4flb_A           90 AAALVK----DPSVSKSVERIFKIWEDRNVYPEEMIVALREALS  129 (132)
T ss_dssp             HHHTTC----STTTHHHHHHHHHHHHHHTSSCHHHHHHHHHHHT
T ss_pred             HHHHhC----CHHHHHHHHHHHHHhccCCCcCHHHHHHHHHHHh
Confidence            566664    6888999999999999999999999999998874

>2km4_A Regulator of TY1 transposition protein 103; CTD-interacting domain, RNA polymerase II binding protein, phosphoprotein; NMR {Saccharomyces cerevisiae} PDB: 2l0i_A*

Probab=95.39  E-value=0.0022  Score=55.07  Aligned_cols=44  Identities=20%  Similarity=0.441  Sum_probs=38.5

Q ss_pred             ccccccccccCCccccccccchhchhhccccchhhHHHHHHHhhh
Q psy15160        181 QAFVSVGDVHCSEKTRSSLSRILNIWEERGVYDKQQIASFRTAFN  225 (366)
Q Consensus       181 ~af~hva~~~~dek~~~~l~r~l~Iw~er~vye~~~i~~~~~~~~  225 (366)
                      .+|.|++.. .|++.++.+.|+++||++|++|+.+++++++..+.
T Consensus        89 ~~~~~~~~~-~~~~~~~kv~rvl~iWeer~vf~~~~i~~L~~~l~  132 (142)
T 2km4_A           89 EVLGRINQE-FPRDLKKKLSRVVNILKERNIFSKQVVNDIERSLA  132 (142)
T ss_dssp             HHHHHHHHH-SCHHHHHHHHHHHHHHHHHTCSCHHHHHHHHHHHH
T ss_pred             HHHHHHHHc-CCHHHHHHHHHHHHHhhccCCcCHHHHHHHHHHHH
Confidence            477788743 58999999999999999999999999999988773

>3d9j_A RNA-binding protein 16; SCAF8, RNA polymerase II CTD interacting domain, arm repeats phospho-CTD, phosphoprotein, transcription; 1.60A {Homo sapiens} PDB: 3d9k_A* 3d9l_A* 3d9m_A* 3d9n_A* 3d9p_A* 3d9i_A 3d9o_A* 2diw_A

Probab=94.21  E-value=0.013  Score=50.52  Aligned_cols=42  Identities=21%  Similarity=0.557  Sum_probs=36.7

Q ss_pred             ccccccccccCCccccccccchhchhhccccchhhHHHHHHHhh
Q psy15160        181 QAFVSVGDVHCSEKTRSSLSRILNIWEERGVYDKQQIASFRTAF  224 (366)
Q Consensus       181 ~af~hva~~~~dek~~~~l~r~l~Iw~er~vye~~~i~~~~~~~  224 (366)
                      .+|.|+.  .++++++..+.|+++||++|++|.+++++.|+..+
T Consensus        94 ~~f~~~~--~~~~~~r~kl~rLl~iW~~r~vF~~~~l~~l~~~l  135 (145)
T 3d9j_A           94 STFQNLY--RCPGDDKSKIVRVLNLWQKNNVFKSEIIQPLLDMA  135 (145)
T ss_dssp             HHHHHHT--SSCGGGHHHHHHHHHHHHHTTSSCHHHHHHHHHHH
T ss_pred             HHHHHHH--hCCHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHh
Confidence            3677776  24699999999999999999999999999999877

>1x5b_A Signal transducing adaptor molecule 2; VHS domain, ubiquitin binding, STAM2, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2l0t_B

Probab=93.37  E-value=0.67  Score=40.43  Aligned_cols=127  Identities=15%  Similarity=0.151  Sum_probs=83.6

Q ss_pred             CCCCCHHHHHHHHHhcccc------HHHHHHHHHHHhhhccchhHHHHHHHHHHhhcCcccchhHHHHhHHHHHHhhhc-
Q psy15160          1 MAGFTQSALISKLEELNAS------QQSIQTLSLWLIHHRKHHSTIVKTWIDEVEKADDHRKLTLMYLANDVIQNSKKK-   73 (366)
Q Consensus         1 M~~Fse~~l~~kL~~L~~S------q~SIqtlS~W~l~h~k~a~~IV~~w~~~L~ka~~~kKL~lLYLaNDVlQnskkk-   73 (366)
                      |--|+...|...+...++.      =..|-.+..-+-.....+.+.+..+.+.|...++...+.-|-|++-+++||-.. 
T Consensus         8 M~~~~~~p~~~~IekATs~~~~~~Dw~~~leicD~I~~~~~~~keA~ral~krl~~~n~~vql~AL~LLd~~vkNcG~~F   87 (163)
T 1x5b_A            8 MPLFTANPFEQDVEKATNEYNTTEDWSLIMDICDKVGSTPNGAKDCLKAIMKRVNHKVPHVALQALTLLGACVANCGKIF   87 (163)
T ss_dssp             CCCCCCCTTHHHHHHHTCTTCSSCCHHHHHHHHHHHHHSSSHHHHHHHHHHHHHTCSSHHHHHHHHHHHHHHHHHTCHHH
T ss_pred             CCCcCCChHHHHHHHHcCCCCCCcCHHHHHHHHHHHhCCCccHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHhhHHH
Confidence            5556666677777766643      344555555555555577889999999998777888888899999999997543 


Q ss_pred             CcchH-HHHHHHHHHHHHHhcccCCChHHHHHHHHHHHHhhhC--CCCCHHHHHHHHHHHH
Q psy15160         74 GPEYG-KEFGHVLKQAFVSVGDVHCSEKTRSSLSRILNIWEER--GVYDKQQIASFRTAFN  131 (366)
Q Consensus        74 g~~f~-~~F~~vL~~af~~i~~~~~d~~~~~kv~RIL~IW~eR--~Vy~~~~i~~L~~~L~  131 (366)
                      ..++. +.|-..|..++.    ...++.++.++..++.-|.+-  +.-.-..|..+...|.
T Consensus        88 h~evas~~Fl~el~~l~~----~~~~~~Vk~kil~li~~W~~~f~~~~~l~~i~~~Y~~Lk  144 (163)
T 1x5b_A           88 HLEVCSRDFATEVRAVIK----NKAHPKVCEKLKSLMVEWSEEFQKDPQFSLISATIKSMK  144 (163)
T ss_dssp             HHHHTSHHHHHHHHHHHH----TTCCHHHHHHHHHHHHHHHHHTTTCSTTHHHHHHHHHHH
T ss_pred             HHHHhhHHHHHHHHHHHc----cCCCHHHHHHHHHHHHHHHHHhcCCcccHHHHHHHHHHH
Confidence            21221 334443444442    234789999999999999972  2222245666666665

>1sz9_A PCF11 protein; RNA polymerase II CTD interacting domain, arm repeats, transcription; 2.10A {Saccharomyces cerevisiae} SCOP: a.118.9.4 PDB: 1sza_A* 2bf0_X

Probab=91.83  E-value=0.034  Score=47.88  Aligned_cols=43  Identities=9%  Similarity=0.325  Sum_probs=38.6

Q ss_pred             ccccccccccCCccccccccchhchhhcc-----ccchhhHHHHHHHhh
Q psy15160        181 QAFVSVGDVHCSEKTRSSLSRILNIWEER-----GVYDKQQIASFRTAF  224 (366)
Q Consensus       181 ~af~hva~~~~dek~~~~l~r~l~Iw~er-----~vye~~~i~~~~~~~  224 (366)
                      .+|.|+. ...|++++..+.|+++||+++     ++|.+++++.|+..+
T Consensus        88 ~~f~~~~-~~~d~~~r~k~~rL~~~W~~~~~~~~~vF~~~~l~~i~~~l  135 (144)
T 1sz9_A           88 NLYKRTY-LLVDNTTRTKLINMFKLWLNPNDTGLPLFEGSALEKIEQFL  135 (144)
T ss_dssp             HHHHHHH-HTSCHHHHHHHHHHHHHHTSGGGCSSCSSCHHHHHHHHHHH
T ss_pred             HHHHHHH-HhCCHHHHHHHHHHHHHHhCcccCCCCCCCHHHHHHHHHHH
Confidence            4788887 457999999999999999999     999999999998877

>4fla_A Regulation of nuclear PRE-mRNA domain-containing 1B; structural genomics consortium, SGC, transcription; 2.20A {Homo sapiens}

Probab=84.46  E-value=9.5  Score=32.95  Aligned_cols=16  Identities=19%  Similarity=0.368  Sum_probs=13.5

Q ss_pred             CCCchhh-hhhHhhhCC
Q psy15160        269 PPEVSEI-QLLSKVQGK  284 (366)
Q Consensus       269 pPEveel-~~L~~Led~  284 (366)
                      ||+|+|| .+|++|+|+
T Consensus        21 p~~~~elik~L~~le~s   37 (152)
T 4fla_A           21 PLLTEELIKALQDLENA   37 (152)
T ss_dssp             --CHHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHhhcc
Confidence            7899999 799999999

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

Original result of RPS-BLAST against SCOP70(version1.75) database

ID	Length	Definition	E-value
Query	366
d1szaa_	144	a.118.9.4 (A:) PCF11 protein {Baker's yeast (Sacch	2e-23

>d1szaa_ a.118.9.4 (A:) PCF11 protein {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 144

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: ENTH/VHS domain
family: RPR domain (SMART 00582 )
domain: PCF11 protein
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 92.4 bits (229), Expect = 2e-23
 Identities = 26/142 (18%), Positives = 45/142 (31%), Gaps = 13/142 (9%)

Query: 1   MAGFTQSAL---ISKLEELN-ASQQSIQTLSLWLIHHRKHHSTIVKTWIDEVEKADDHRK 56
           M   T+  +    S LEEL   S+  I TL+     +       V      +EK    +K
Sbjct: 1   MDHDTEVIVKDFNSILEELTFNSRPIITTLTKLAEENISCAQYFVDAIESRIEKCMPKQK 60

Query: 57  LTLMYLANDVIQNSKKKGPEYGKEFGHVLKQAFVSVGDVHCSEKTRSSLSRILNIWEERG 116
           L   Y  + + +N       Y   F   L   +     +     TR+ L  +  +W    
Sbjct: 61  LYAFYALDSICKNVG---SPYTIYFSRNLFNLYKRT-YLLVDNTTRTKLINMFKLWLNPN 116

Query: 117 -----VYDKQQIASFRTAFNAA 133
                +++   +         A
Sbjct: 117 DTGLPLFEGSALEKIEQFLIKA 138

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	366
d1szaa_	144	PCF11 protein {Baker's yeast (Saccharomyces cerevi	99.94
d1szaa_	144	PCF11 protein {Baker's yeast (Saccharomyces cerevi	90.17
d1dvpa1	145	Hrs {Fruit fly (Drosophila melanogaster) [TaxId: 7	84.45
d1ujka_	145	ADP-ribosylation factor binding protein Gga1 {Huma	81.16

>d1szaa_ a.118.9.4 (A:) PCF11 protein {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: ENTH/VHS domain
family: RPR domain (SMART 00582 )
domain: PCF11 protein
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.94  E-value=9.9e-27  Score=201.09  Aligned_cols=124  Identities=20%  Similarity=0.282  Sum_probs=116.5

Q ss_pred             HHHHHHHHHhcc-ccHHHHHHHHHHHhhhccchhHHHHHHHHHHhhcCcccchhHHHHhHHHHHHhhhcCcchHHHHHHH
Q psy15160          6 QSALISKLEELN-ASQQSIQTLSLWLIHHRKHHSTIVKTWIDEVEKADDHRKLTLMYLANDVIQNSKKKGPEYGKEFGHV   84 (366)
Q Consensus         6 e~~l~~kL~~L~-~Sq~SIqtlS~W~l~h~k~a~~IV~~w~~~L~ka~~~kKL~lLYLaNDVlQnskkkg~~f~~~F~~v   84 (366)
                      .+.|...|++|+ +|+..|++|+.|+++|++++..||++|.+++.++++++||++|||+|||+|||   +++|...|+++
T Consensus         9 ~~~f~~~L~~L~~ns~~~I~~Lt~~a~~~~~~a~~Iv~~i~~~i~~~~~~~KL~~LYLiddI~~n~---~~~y~~~f~~~   85 (144)
T d1szaa_           9 VKDFNSILEELTFNSRPIITTLTKLAEENISCAQYFVDAIESRIEKCMPKQKLYAFYALDSICKNV---GSPYTIYFSRN   85 (144)
T ss_dssp             HHHHHHHHTTCSSCCHHHHHHHHHHHHHCGGGHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHT---CTTHHHHHHTT
T ss_pred             HHHHHHHHHHHhhccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCcccchhhhhhHHHHHHHh---HHHHHHHHHHH
Confidence            356899999997 79999999999999999999999999999999999999999999999999998   45799999999


Q ss_pred             HHHHHHHhcccCCChHHHHHHHHHHHHhhhCC-----CCCHHHHHHHHHHHHhh
Q psy15160         85 LKQAFVSVGDVHCSEKTRSSLSRILNIWEERG-----VYDKQQIASFRTAFNAA  133 (366)
Q Consensus        85 L~~af~~i~~~~~d~~~~~kv~RIL~IW~eR~-----Vy~~~~i~~L~~~L~~~  133 (366)
                      ||.+|.+++ ...++.++.++.||+++|++|+     ||+++++..|+..|.+.
T Consensus        86 l~~~f~~~y-~~~~~~~r~kl~rll~iW~~r~~~~~~vFp~~~l~~ie~~L~~a  138 (144)
T d1szaa_          86 LFNLYKRTY-LLVDNTTRTKLINMFKLWLNPNDTGLPLFEGSALEKIEQFLIKA  138 (144)
T ss_dssp             HHHHHHHHH-TTSCHHHHHHHHHHHHHHSSGGGCSSCSSCHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHH-HcCCHHHHHHHHHHHHHHhccCCCCcCCCCHHHHHHHHHHHHHh
Confidence            999999999 5789999999999999999988     99999999999999733

>d1szaa_ a.118.9.4 (A:) PCF11 protein {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: ENTH/VHS domain
family: RPR domain (SMART 00582 )
domain: PCF11 protein
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=90.17  E-value=0.031  Score=45.82  Aligned_cols=42  Identities=10%  Similarity=0.343  Sum_probs=36.5

Q ss_pred             cccccccccCCccccccccchhchhhccc-----cchhhHHHHHHHhh
Q psy15160        182 AFVSVGDVHCSEKTRSSLSRILNIWEERG-----VYDKQQIASFRTAF  224 (366)
Q Consensus       182 af~hva~~~~dek~~~~l~r~l~Iw~er~-----vye~~~i~~~~~~~  224 (366)
                      +|.|++ ...|+.++..+.|+++||++|+     +|+.+++..++..+
T Consensus        89 ~f~~~y-~~~~~~~r~kl~rll~iW~~r~~~~~~vFp~~~l~~ie~~L  135 (144)
T d1szaa_          89 LYKRTY-LLVDNTTRTKLINMFKLWLNPNDTGLPLFEGSALEKIEQFL  135 (144)
T ss_dssp             HHHHHH-TTSCHHHHHHHHHHHHHHSSGGGCSSCSSCHHHHHHHHHHH
T ss_pred             HHHHHH-HcCCHHHHHHHHHHHHHHhccCCCCcCCCCHHHHHHHHHHH
Confidence            677766 4668999999999999999998     89999999998777

>d1dvpa1 a.118.9.2 (A:1-145) Hrs {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: ENTH/VHS domain
family: VHS domain
domain: Hrs
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=84.45  E-value=1.6  Score=35.01  Aligned_cols=120  Identities=13%  Similarity=0.140  Sum_probs=78.4

Q ss_pred             HHHHHHHhccc------cHHHHHHHHHHHhhhccchhHHHHHHHHHHhhcCcccchhHHHHhHHHHHHhhhc-Ccch-HH
Q psy15160          8 ALISKLEELNA------SQQSIQTLSLWLIHHRKHHSTIVKTWIDEVEKADDHRKLTLMYLANDVIQNSKKK-GPEY-GK   79 (366)
Q Consensus         8 ~l~~kL~~L~~------Sq~SIqtlS~W~l~h~k~a~~IV~~w~~~L~ka~~~kKL~lLYLaNDVlQnskkk-g~~f-~~   79 (366)
                      .|+..+...|+      -=+.|-.+..-+-.....+...+.++.+.|...++...+.-|.|+.-++.||-.. +.++ ..
T Consensus         5 ~~~~~iekAT~~~~~~~dw~~il~icD~I~~~~~~~k~a~ral~krl~~~n~~v~l~aL~LLd~~vkNcG~~f~~~i~s~   84 (145)
T d1dvpa1           5 SFCKNLENATSHLRLEPDWPSILLICDEINQKDVTPKNAFAAIKKKMNSPNPHSSCYSLLVLESIVKNCGAPVHEEVFTK   84 (145)
T ss_dssp             HHHHHHHHHHCTTCSSCCHHHHHHHHHHHHTTSSCHHHHHHHHHHHHTCSSHHHHHHHHHHHHHHHHHSHHHHHHHHSSH
T ss_pred             hHHHHHHHHcCcCCCCCCHHHHHHHHHHHhCCCccHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHccchHHHHHHhhH
Confidence            45555555442      2456666777666566678999999999998888888899999999999998654 2211 22


Q ss_pred             HHHHHHHHHHHHhcccCCChHHHHHHHHHHHHhhhC--CCCCHHHHHHHHHHHH
Q psy15160         80 EFGHVLKQAFVSVGDVHCSEKTRSSLSRILNIWEER--GVYDKQQIASFRTAFN  131 (366)
Q Consensus        80 ~F~~vL~~af~~i~~~~~d~~~~~kv~RIL~IW~eR--~Vy~~~~i~~L~~~L~  131 (366)
                      .|-..|..++.    ...+..++.++..++..|.+-  +--+-..+..+...|.
T Consensus        85 ~fl~~l~~l~~----~~~~~~Vk~kil~li~~W~~~f~~~~~~~~i~~~y~~Lk  134 (145)
T d1dvpa1          85 ENCEMFSSFLE----STPHENVRQKMLELVQTWAYAFRSSDKYQAIKDTMTILK  134 (145)
T ss_dssp             HHHHHHHHHHH----HCSCHHHHHHHHHHHHHHHHHTTTCSSCCHHHHHHHHHH
T ss_pred             HHHHHHHHHhc----CCCCHHHHHHHHHHHHHHHHHhCCCccchHHHHHHHHHH
Confidence            33333333332    344678999999999999983  2212233555554453

>d1ujka_ a.118.9.2 (A:) ADP-ribosylation factor binding protein Gga1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: ENTH/VHS domain
family: VHS domain
domain: ADP-ribosylation factor binding protein Gga1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=81.16  E-value=1.1  Score=36.20  Aligned_cols=110  Identities=12%  Similarity=0.147  Sum_probs=67.2

Q ss_pred             CHHHHHHHHHhccc---c---HHHHHHHHHHHhhhccchhHHHHHHHHHHhhcCcccchhHHHHhHHHHHHhhhc-Ccch
Q psy15160          5 TQSALISKLEELNA---S---QQSIQTLSLWLIHHRKHHSTIVKTWIDEVEKADDHRKLTLMYLANDVIQNSKKK-GPEY   77 (366)
Q Consensus         5 se~~l~~kL~~L~~---S---q~SIqtlS~W~l~h~k~a~~IV~~w~~~L~ka~~~kKL~lLYLaNDVlQnskkk-g~~f   77 (366)
                      .+..|+..+...|+   +   -+.|-.+..-+-.....+...+.++.+.|...++...+.-|.|+.-++.||-.. ..++
T Consensus         5 ~~~~~e~~iekAT~~~l~~~dw~~ileicD~I~~~~~~~k~a~r~l~krl~~~~~~~~l~aL~LLe~~vkNCG~~f~~ev   84 (145)
T d1ujka_           5 EPETLEARINRATNPLNKELDWASINGFCEQLNEDFEGPPLATRLLAHKIQSPQEWEAIQALTVLETCMKSCGKRFHDEV   84 (145)
T ss_dssp             STTSHHHHHHHHTCTTCSSCCHHHHHHHHHHHTSSTTHHHHHHHHHHHHHTCSSHHHHHHHHHHHHHHHTSCCHHHHHHH
T ss_pred             CcchHHHHHHHHcCCCCCCcCHHHHHHHHHHHhCCCccHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHhHHHHHHH
Confidence            44556666655542   2   344445555444444557888899999987767777777788888888776332 1111


Q ss_pred             -HHHHHHHHHHHHHHhcc-cCCChHHHHHHHHHHHHhhh
Q psy15160         78 -GKEFGHVLKQAFVSVGD-VHCSEKTRSSLSRILNIWEE  114 (366)
Q Consensus        78 -~~~F~~vL~~af~~i~~-~~~d~~~~~kv~RIL~IW~e  114 (366)
                       ...|-..|..++..-+. ...+..++.++..++..|.+
T Consensus        85 as~~Fl~~L~kli~~k~~~~~~~~~Vk~kil~li~~W~~  123 (145)
T d1ujka_          85 GKFRFLNELIKVVSPKYLGSRTSEKVKNKILELLYSWTV  123 (145)
T ss_dssp             TSHHHHHHHHHHHCTTTTGGGSCHHHHHHHHHHHHHHHH
T ss_pred             hhHHHHHHHHHHHhhccCCCCCcHHHHHHHHHHHHHHHH
Confidence             22344444444432110 23467899999999999986